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Predicting splicing effects of human genome variants from sequences

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iDARTS: individualized Deep-learning Analysis of RNA Transcript Splicing

Table of Contents

Installation

Installation of the required packages can be easy by using Miniconda.

Install required packages

conda create -n idarts python=2.7 --solver=classic 
conda activate idarts
conda install tensorflow==1.9.0 -c conda-forge --solver=classic 
conda install keras==2.2.4 -c conda-forge --solver=classic 
conda install viennarna==2.2.10 -c bioconda --solver=classic 
conda install bedtools -c bioconda --solver=classic 
conda install pysam -c bioconda --solver=classic 
conda install pandas -c conda-forge --solver=classic 
conda install regex -c conda-forge --solver=classic 
conda install pyyaml -c conda-forge --solver=classic 
conda install pyBigWig -c bioconda --solver=classic 
conda install cyvcf2 -c bioconda --solver=classic 

pip install scikit-image
pip install psutil
pip install joblib
pip install tqdm

If the installation takes a long time, we have provided an environment file for installation.

git clone https://github.com/xinglab/iDARTS
cd iDARTS

conda env create -n idarts -f environment.yml --solver=classic

Clone the repository and then download resource files

# if you have already cloned the repository, please skip this step
# clone the repository
git clone https://github.com/xinglab/iDARTS

# download resources
cd iDARTS
# change the permission of iDARTS (on Linux server)
chmod +x ./bin/iDARTS
./bin/iDARTS get_resources -o /path/to/directory/

Usage

iDARTS allows users to input a Variant Call Format (VCF) file containing variants of interest and make predictions on either pre-compiled (annotated) or user-provided alternative splicing (AS) events. These predictions are based on the iDARTS deep neural network (DNN), trained on GTEx data, and reference RNA-binding protein (RBP) expression levels across 53 GTEx tissues. The software outputs include:

  • Predicted splicing levels (PSI values) of the reference and variant alleles.
  • Predicted variant effects on splicing (ΔPSI) in GTEx tissue types.

Additionally, iDARTS can make predictions based on user-provided RBP expression levels for specific sample types of interest. When a VCF file is not provided, iDARTS reports predicted splicing levels (PSI values) for AS events of interest.

Predicting effects of variants on splicing

iDARTS is a robust and flexible computational framework for quantitative prediction of alternative splicing (AS) profiles. It can take several types of inputs.

Input:

  • Option 1. User-provided VCF file

    • The pre-compiled AS events and RBP expression levels across 53 GTEx tissues will be used for prediction.

  • Option 2. User-provided VCF file and AS events

    • The pre-compiled RBP expression levels across 53 GTEx tissues will be used for prediction.
    • iDARTS can make predictions for SE, A3SS, and A5SS. The format of each AS type can be found in rmats-turbo. More specifically:
      • Shared columns:
        • ID: rMATS event id
        • GeneID: Gene id
        • geneSymbol: Gene name
        • chr: Chromosome
        • strand: Strand of the gene
      • SE: exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
        • The inclusion form includes the target exon (exonStart_0base, exonEnd)
      • A3SS, A5SS: longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
        • The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)

  • Option 3. User-provided VCF file, AS events, and RBP expression levels for specific sample types of interest

    • The preparation of AS events can be found in the above Option 2.
    • iDARTS can make predictions for specific sample types of interest. This is enabled by preparing input gene expression file (TPM values quantified by Kallisto).
    • The format of gene expression file:
      • Column Name
        • GeneID: Gene id
        • Sample1,Sample2,Sample3,...: Expression levels of different samples separated by comma

Output:

iDARTS outputs two result files with user-defined file name prefix:

No. File Name Description
1 output_file_name_prefix.vcf The output VCF file contains information of each variant and its predicted ΔPSI with the maximum absolute value across all provided mapped splicing events in tissue or samples. (iDARTS will make predictions only if variants are within 300nt of target exons.)
2 output_file_name_prefix.iDARTS_prediction The output iDARTS prediction file provides predicted splicing levels and ΔPSI across all tissues or samples for each variant in each splicing event as well as predicted splicing levels in each tissue or sample.

1. output_file_name_prefix.vcf

  • CHROM: Chromosome name
  • POS: Position
  • ID: SNP ID
  • REF: Reference allele
  • ALT: Alternative allele
  • QUAL: Not provided
  • FILTER: Not provided
  • INFO: iDARTS=AS type|Predicted ΔPSI.
    • The predicted ΔPSI shows the maximum effect of the variant on splicing when considering all mapped AS events in samples.
    • For SE events, if the predicted ΔPSI is positive, the variant causes higher inclusion for the target exon, and if the predicted ΔPSI is negative, the variant causes lower inclusion for the target exon.
    • For A3SS/A5SS events, if the predicted ΔPSI is positive, the variant causes higher inclusion for the longer exon, and if the predicted ΔPSI is negative, the variant causes lower inclusion for the longer exon.

2. output_file_name_prefix.iDARTS_prediction

Shared columns:

  • SNP_ID: SNP ID of the variant
  • max_deltaPSI: The predicted ΔPSI with the maximum absolute value across all samples for each variant and AS event pair. This score can be used to investigate the effects of variants on specific splicing events.
  • Pos0base: The position of the variant (0-based)
  • Ref: Reference allele of the variant
  • Alt: Alternative allele of the variant
  • GeneID: Gene ID
  • geneSymbol: Gene name
  • chr: Chromosome name
  • strand: strand of the gene

AS event specific columns:

  • SE: exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
    • The inclusion form includes the target exon (exonStart_0base, exonEnd)
  • A3SS, A5SS: longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
    • The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)

iDARTS Prediction columns: (Suppose we have three samples with sample name Sample1, Sample2, and Sample3 specified in user-provided RBP expression levels of sample types. When not provided, the RBP expression levels across 53 GTEx tissues will be used.)

  • Sample1_ref_PSI: The predicted reference PSI of the target AS event in Sample1
  • Sample2_ref_PSI: The predicted reference PSI of the target AS event in Sample2
  • Sample3_ref_PSI: The predicted reference PSI of the target AS event in Sample3
  • Sample1_deltaPSI: The predicted ΔPSI of the target AS event in Sample1
  • Sample2_deltaPSI: The predicted ΔPSI of the target AS event in Sample2
  • Sample3_deltaPSI: The predicted ΔPSI of the target AS event in Sample3

Example

Example 1:

Input: User-provided VCF file

  • VCF file needs to be sorted and have an index file that ends with .idx.
  • Example code:
bcftools sort ./example/example.vcf > ./example/example.sorted.vcf
bgzip ./example/example.sorted.vcf
tabix -p vcf ./example/example.sorted.vcf.gz

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing

./bin/iDARTS parse_vcf -v ./example/example.sorted.vcf.gz -t SE -o ./example/example_iDARTS_pred

Example 2:

Input: User-provided VCF file and AS events

  • VCF file needs to be sorted (Please see Example 1 for more details).
  • The example of SE event can be found in ./example/example.SE_events.txt.

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing using user-provided AS events

./bin/iDARTS parse_vcf -v ./example/example.sorted.vcf.gz -t SE -i ./example/example.SE_events.txt -o ./example/example_iDARTS_pred

Example 3:

Input: User-provided VCF file, AS events, and RBP expression levels for specific sample types of interest

  • VCF file needs to be sorted (Please see Example 1 for more details).
  • The example of SE event can be found in ./example/example.SE_events.txt.
  • The example of RBP expression levels for different samples (here we take 53 tissues and cell types in GTEx as examples) can be found in ./example/example.RBP_expression_in_tissues.txt.

Process the sorted VCF file and predict the effects of variants in the VCF file on splicing using user-provided AS events and RBP expression levels

./bin/iDARTS parse_vcf -v ./example/example.sorted.vcf.gz -t SE -i ./example/example.SE_events.txt -e ./example/example.RBP_expression_in_tissues.txt -o ./example/example_iDARTS_pred

Output (Example1, Example2, and Example3):

Example1, Example2, and Example3 have the same output.

  1. ./example/example_iDARTS_pred.vcf
##fileformat=VCFv4.2
##fileDate=20220907
##reference=GRCh37/hg19
##INFO=<ID=iDARTS,Number=.,Type=String,Description="iDARTS variant prediction. Maximum absolute deltaPSI across all tissues">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
2	110905531	2_110905531_C_T_b37	C	T	.	.	iDARTS=SE|-0.212
2	166854706	2_166854706_G_C_b37	G	C	.	.	iDARTS=SE|-0.2885
5	112102045	5_112102045_G_T_b37	G	T	.	.	iDARTS=SE|-0.4181
8	68066380	8_68066380_C_G_b37	C	G	.	.	iDARTS=SE|-0.1084
11	47369212	11_47369212_G_C_b37	G	C	.	.	iDARTS=SE|-0.3383
11	94219111	11_94219111_G_A_b37	G	A	.	.	iDARTS=SE|-0.3088
13	52535985	13_52535985_A_C_b37	A	C	.	.	iDARTS=SE|-0.0915
14	73637762	14_73637762_A_G_b37	A	G	.	.	iDARTS=SE|-0.2253
16	 2098764	  16_2098764_C_G_b37	C	G	.	.	iDARTS=SE|-0.1588
X	135112295	X_135112295_G_A_b37	G	A	.	.	iDARTS=SE|-0.2213
  1. ./example/example_iDARTS_pred.iDARTS_prediction
SNP_ID max_deltaPSI Pos0base Ref Alt GeneID geneSymbol chr strand exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE Adipose - Subcutaneous_ref_PSI Adipose - Visceral (Omentum)_ref_PSI Adrenal Gland_ref_PSI Artery - Aorta_ref_PSI Artery - Coronary_ref_PSI Artery - Tibial_ref_PSI Bladder_ref_PSI Brain - Amygdala_ref_PSI Brain - Anterior cingulate cortex (BA24)_ref_PSI Brain - Caudate (basal ganglia)_ref_PSI Brain - Cerebellar Hemisphere_ref_PSI Brain - Cerebellum_ref_PSI Brain - Cortex_ref_PSI Brain - Frontal Cortex (BA9)_ref_PSI Brain - Hippocampus_ref_PSI Brain - Hypothalamus_ref_PSI Brain - Nucleus accumbens (basal ganglia)_ref_PSI Brain - Putamen (basal ganglia)_ref_PSI Brain - Spinal cord (cervical c-1)_ref_PSI Brain - Substantia nigra_ref_PSI Breast - Mammary Tissue_ref_PSI Cells - Cultured fibroblasts_ref_PSI Cells - EBV-transformed lymphocytes_ref_PSI Cervix - Ectocervix_ref_PSI Cervix - Endocervix_ref_PSI Colon - Sigmoid_ref_PSI Colon - Transverse_ref_PSI Esophagus - Gastroesophageal Junction_ref_PSI Esophagus - Mucosa_ref_PSI Esophagus - Muscularis_ref_PSI Fallopian Tube_ref_PSI Heart - Atrial Appendage_ref_PSI Heart - Left Ventricle_ref_PSI Kidney - Cortex_ref_PSI Liver_ref_PSI Lung_ref_PSI Minor Salivary Gland_ref_PSI Muscle - Skeletal_ref_PSI Nerve - Tibial_ref_PSI Ovary_ref_PSI Pancreas_ref_PSI Pituitary_ref_PSI Prostate_ref_PSI Skin - Not Sun Exposed (Suprapubic)_ref_PSI Skin - Sun Exposed (Lower leg)_ref_PSI Small Intestine - Terminal Ileum_ref_PSI Spleen_ref_PSI Stomach_ref_PSI Testis_ref_PSI Thyroid_ref_PSI Uterus_ref_PSI Vagina_ref_PSI Whole Blood_ref_PSI Adipose - Subcutaneous_deltaPSI Adipose - Visceral (Omentum)_deltaPSI Adrenal Gland_deltaPSI Artery - Aorta_deltaPSI Artery - Coronary_deltaPSI Artery - Tibial_deltaPSI Bladder_deltaPSI Brain - Amygdala_deltaPSI Brain - Anterior cingulate cortex (BA24)_deltaPSI Brain - Caudate (basal ganglia)_deltaPSI Brain - Cerebellar Hemisphere_deltaPSI Brain - Cerebellum_deltaPSI Brain - Cortex_deltaPSI Brain - Frontal Cortex (BA9)_deltaPSI Brain - Hippocampus_deltaPSI Brain - Hypothalamus_deltaPSI Brain - Nucleus accumbens (basal ganglia)_deltaPSI Brain - Putamen (basal ganglia)_deltaPSI Brain - Spinal cord (cervical c-1)_deltaPSI Brain - Substantia nigra_deltaPSI Breast - Mammary Tissue_deltaPSI Cells - Cultured fibroblasts_deltaPSI Cells - EBV-transformed lymphocytes_deltaPSI Cervix - Ectocervix_deltaPSI Cervix - Endocervix_deltaPSI Colon - Sigmoid_deltaPSI Colon - Transverse_deltaPSI Esophagus - Gastroesophageal Junction_deltaPSI Esophagus - Mucosa_deltaPSI Esophagus - Muscularis_deltaPSI Fallopian Tube_deltaPSI Heart - Atrial Appendage_deltaPSI Heart - Left Ventricle_deltaPSI Kidney - Cortex_deltaPSI Liver_deltaPSI Lung_deltaPSI Minor Salivary Gland_deltaPSI Muscle - Skeletal_deltaPSI Nerve - Tibial_deltaPSI Ovary_deltaPSI Pancreas_deltaPSI Pituitary_deltaPSI Prostate_deltaPSI Skin - Not Sun Exposed (Suprapubic)_deltaPSI Skin - Sun Exposed (Lower leg)_deltaPSI Small Intestine - Terminal Ileum_deltaPSI Spleen_deltaPSI Stomach_deltaPSI Testis_deltaPSI Thyroid_deltaPSI Uterus_deltaPSI Vagina_deltaPSI Whole Blood_deltaPSI
11_47369212_G_C_b37 0.0415 47369211 G C ENSG00000134571.10_2 MYBPC3 chr11 - 47368976 47369030 47368177 47368198 47369201 47369231 0.8497 0.8574 0.8544 0.8279 0.8405 0.8359 0.8289 0.8615 0.8621 0.8682 0.8274 0.8208 0.8486 0.8626 0.8648 0.8665 0.8512 0.8712 0.846 0.8688 0.8594 0.851 0.8732 0.8492 0.8482 0.8563 0.8675 0.8551 0.8384 0.845 0.8433 0.8584 0.8759 0.8584 0.883 0.8498 0.8602 0.851 0.8654 0.8492 0.8793 0.8712 0.8462 0.8577 0.8551 0.8714 0.893 0.875 0.8402 0.874 0.8356 0.8431 0.8747 0.0307 0.0302 0.0282 0.0342 0.0289 0.0287 0.0336 0.0244 0.0237 0.0229 0.0261 0.0287 0.0311 0.0224 0.0231 0.0225 0.0266 0.0243 0.0329 0.0229 0.0278 0.0328 0.0288 0.0258 0.028 0.0314 0.0335 0.0282 0.0415 0.0287 0.0284 0.0293 0.0239 0.03 0.0286 0.0311 0.0326 0.0272 0.0292 0.0261 0.0215 0.0239 0.0351 0.0321 0.0344 0.0247 0.02 0.0266 0.04 0.0156 0.0337 0.0295 0.029
11_47369212_G_C_b37 -0.3383 47369211 G C ENSG00000134571.10_2 MYBPC3 chr11 - 47369201 47369231 47368976 47369030 47369407 47369456 0.839 0.8344 0.8299 0.822 0.8219 0.7968 0.8307 0.818 0.817 0.8207 0.7236 0.7513 0.8097 0.8212 0.8254 0.8163 0.8183 0.8214 0.8376 0.8166 0.8544 0.7868 0.8149 0.8301 0.8091 0.8348 0.8299 0.8375 0.8355 0.8295 0.8236 0.8043 0.7973 0.8217 0.8336 0.8344 0.8528 0.7971 0.8224 0.7987 0.8464 0.8381 0.8384 0.8356 0.8355 0.8396 0.8432 0.8382 0.7605 0.8021 0.8142 0.8481 0.8321 -0.3105 -0.3283 -0.3103 -0.291 -0.2923 -0.2902 -0.2883 -0.3033 -0.2945 -0.284 -0.2349 -0.2443 -0.2752 -0.2754 -0.2977 -0.2802 -0.2795 -0.2962 -0.2929 -0.2902 -0.2851 -0.3211 -0.2998 -0.2784 -0.2792 -0.32 -0.3092 -0.3201 -0.3252 -0.327 -0.2575 -0.3381 -0.3383 -0.3326 -0.3135 -0.2762 -0.3185 -0.331 -0.2545 -0.2564 -0.2974 -0.2653 -0.2857 -0.2815 -0.283 -0.2728 -0.2413 -0.3314 -0.2552 -0.2802 -0.2601 -0.2814 -0.3211
11_47369212_G_C_b37 0.0111 47369211 G C ENSG00000134571.10_2 MYBPC3 chr11 - 47369407 47369456 47369201 47369231 47369974 47370092 0.9499 0.95 0.9609 0.9508 0.9527 0.9512 0.9565 0.9449 0.9356 0.9404 0.912 0.9122 0.9298 0.9293 0.9466 0.9395 0.9324 0.9457 0.9508 0.9491 0.9515 0.9571 0.9537 0.9566 0.9459 0.9569 0.9533 0.9555 0.9559 0.9551 0.9333 0.9453 0.9507 0.9527 0.9577 0.9439 0.95 0.9386 0.9389 0.9419 0.9585 0.9386 0.9523 0.9454 0.9453 0.9542 0.9587 0.9546 0.9155 0.9441 0.9469 0.9511 0.9539 0.0039 0.0035 0.0024 0.0051 0.0029 0.0036 0.004 0.0023 0.0064 0.0051 0.0033 0.002 0.0075 0.0068 0.0027 0.005 0.0061 0.004 0.0046 0.0048 0.0029 0.0055 0.0037 0.0017 0.0011 0.0052 0.0063 0.0069 0.007 0.0077 0.0086 0.0068 0.0069 0.0041 0.004 0.0053 0.005 0.01 0.0074 0.0091 0.0031 0.0065 0.0045 0.0067 0.0065 0.0065 0.0039 0.0032 0.0111 0.0057 0.0038 0.0041 0.0054
11_94219111_G_A_b37 -0.3088 94219110 G A ENSG00000020922.12_3 MRE11 chr11 - 94219089 94219250 94211926 94212042 94223998 94224131 0.6638 0.6536 0.6856 0.6819 0.6772 0.663 0.6898 0.6026 0.6257 0.6386 0.6033 0.6459 0.6592 0.6277 0.6231 0.6148 0.6044 0.6571 0.6444 0.6338 0.6587 0.6448 0.6046 0.6537 0.6442 0.7079 0.6749 0.7007 0.6763 0.7179 0.6368 0.6378 0.6413 0.6335 0.617 0.6488 0.6978 0.6295 0.6834 0.6118 0.6382 0.6254 0.6495 0.634 0.6476 0.6448 0.7065 0.6524 0.5949 0.6353 0.6318 0.6659 0.6323 -0.2699 -0.291 -0.2659 -0.2711 -0.2926 -0.2481 -0.2522 -0.2341 -0.2316 -0.2422 -0.1817 -0.1966 -0.2336 -0.2216 -0.2424 -0.2427 -0.2299 -0.2533 -0.2551 -0.2626 -0.2825 -0.267 -0.2456 -0.26 -0.2511 -0.2837 -0.2809 -0.2862 -0.29 -0.2889 -0.2385 -0.2929 -0.2927 -0.2768 -0.2721 -0.277 -0.3088 -0.2675 -0.2598 -0.2386 -0.2582 -0.2233 -0.2631 -0.295 -0.2874 -0.2693 -0.2693 -0.2738 -0.1693 -0.2674 -0.2393 -0.2776 -0.2531
11_94219111_G_A_b37 -0.1013 94219110 G A ENSG00000020922.12_3 MRE11 chr11 - 94219089 94219250 94212839 94212927 94223998 94224131 0.9452 0.9504 0.9496 0.9448 0.9501 0.9352 0.9349 0.9195 0.9189 0.9231 0.8398 0.8669 0.9194 0.9218 0.9202 0.9276 0.9138 0.925 0.9199 0.933 0.937 0.9471 0.9195 0.9186 0.9134 0.9394 0.9472 0.9449 0.9407 0.9479 0.9131 0.9509 0.9482 0.9348 0.942 0.9358 0.9514 0.9478 0.9116 0.8988 0.9391 0.9166 0.9259 0.9332 0.936 0.9393 0.9382 0.9446 0.8534 0.9086 0.9058 0.9261 0.9238 -0.0605 -0.0604 -0.0609 -0.0629 -0.0567 -0.0683 -0.0668 -0.0792 -0.0691 -0.0688 -0.1013 -0.0878 -0.0623 -0.0629 -0.0751 -0.0688 -0.0777 -0.0713 -0.0702 -0.0727 -0.0709 -0.0665 -0.0918 -0.0841 -0.0879 -0.0723 -0.0653 -0.0677 -0.0707 -0.0617 -0.0818 -0.0613 -0.0626 -0.0698 -0.0754 -0.0672 -0.0562 -0.0565 -0.0849 -0.0851 -0.0608 -0.0802 -0.0812 -0.0712 -0.07 -0.0669 -0.0623 -0.0641 -0.0984 -0.0952 -0.0886 -0.0737 -0.0772
11_94219111_G_A_b37 -0.0933 94219110 G A ENSG00000020922.12_3 MRE11 chr11 - 94219089 94219250 94212860 94212927 94223998 94224131 0.9513 0.9545 0.9557 0.9509 0.9555 0.9426 0.9434 0.925 0.9266 0.9294 0.8528 0.8779 0.9236 0.9264 0.9268 0.9332 0.9212 0.9325 0.9294 0.9385 0.9426 0.9548 0.9253 0.9277 0.9229 0.947 0.952 0.9504 0.9465 0.9534 0.9246 0.9561 0.9542 0.9415 0.9469 0.942 0.9563 0.9499 0.9207 0.9095 0.9453 0.9256 0.9316 0.9377 0.9424 0.9443 0.9427 0.9503 0.8643 0.9175 0.9159 0.9344 0.9318 -0.0512 -0.0493 -0.0524 -0.0539 -0.0484 -0.0586 -0.0594 -0.068 -0.065 -0.0619 -0.0933 -0.0821 -0.0589 -0.0611 -0.0658 -0.0618 -0.0698 -0.0651 -0.0617 -0.064 -0.0627 -0.0576 -0.0824 -0.0746 -0.0821 -0.0625 -0.0569 -0.0567 -0.0621 -0.0526 -0.0734 -0.0513 -0.0523 -0.0616 -0.0667 -0.0583 -0.0484 -0.0519 -0.077 -0.077 -0.0546 -0.0725 -0.0691 -0.0604 -0.0618 -0.0596 -0.0556 -0.0547 -0.0921 -0.0822 -0.0784 -0.0641 -0.0658
11_94219111_G_A_b37 -0.1929 94219110 G A ENSG00000020922.12_3 MRE11 chr11 - 94219089 94219250 94212908 94212927 94223998 94224131 0.864 0.8675 0.8837 0.8767 0.88 0.8612 0.8608 0.8504 0.8532 0.8569 0.7744 0.8023 0.8556 0.8453 0.856 0.8616 0.8405 0.8638 0.8612 0.8693 0.8606 0.8724 0.8129 0.8446 0.8371 0.8635 0.8807 0.8815 0.8742 0.8876 0.835 0.8974 0.8878 0.8679 0.8579 0.8614 0.8962 0.8501 0.8459 0.7855 0.8736 0.8408 0.8603 0.8602 0.8667 0.8651 0.8641 0.8815 0.7505 0.8321 0.821 0.8558 0.8272 -0.1687 -0.1724 -0.1308 -0.1603 -0.1447 -0.1541 -0.1638 -0.1518 -0.149 -0.1384 -0.1486 -0.128 -0.13 -0.1408 -0.1432 -0.1412 -0.146 -0.1376 -0.1521 -0.1516 -0.16 -0.1647 -0.1929 -0.1728 -0.1682 -0.1625 -0.152 -0.1486 -0.1689 -0.1445 -0.1725 -0.1462 -0.1429 -0.1511 -0.1754 -0.1551 -0.1514 -0.1525 -0.156 -0.1641 -0.1601 -0.1459 -0.1468 -0.1687 -0.1517 -0.1579 -0.1499 -0.1429 -0.1479 -0.1831 -0.1686 -0.1756 -0.1686
11_94219111_G_A_b37 -0.2786 94219110 G A ENSG00000020922.12_3 MRE11 chr11 - 94219089 94219250 94216935 94217005 94223998 94224131 0.746 0.7239 0.7774 0.7793 0.7713 0.7494 0.7751 0.7003 0.7067 0.7127 0.6447 0.675 0.7302 0.7074 0.7125 0.6979 0.6819 0.7323 0.7179 0.7223 0.7292 0.7311 0.6801 0.7373 0.7077 0.7742 0.7476 0.7741 0.728 0.7808 0.7362 0.7321 0.7466 0.7271 0.7168 0.7074 0.7709 0.7321 0.746 0.6566 0.7348 0.6685 0.723 0.726 0.7359 0.7188 0.7471 0.7514 0.6314 0.6989 0.7036 0.7633 0.7294 -0.2665 -0.2728 -0.2527 -0.2608 -0.277 -0.2561 -0.2584 -0.2248 -0.2039 -0.2177 -0.1693 -0.1724 -0.2077 -0.1986 -0.2276 -0.2162 -0.2054 -0.2262 -0.2238 -0.2302 -0.2599 -0.2507 -0.2331 -0.2542 -0.2514 -0.2473 -0.2558 -0.2512 -0.2532 -0.2362 -0.2455 -0.2534 -0.2506 -0.2599 -0.2664 -0.2539 -0.2786 -0.2363 -0.2492 -0.2097 -0.2409 -0.2116 -0.2458 -0.2756 -0.2545 -0.2417 -0.2241 -0.2506 -0.1666 -0.2518 -0.241 -0.2662 -0.2447
13_52535985_A_C_b37 -0.0765 52535984 A C ENSG00000123191.14_3 ATP7B chr13 - 52535972 52536049 52531651 52534458 52539007 52539169 0.7471 0.7419 0.8106 0.728 0.7591 0.7099 0.7807 0.7235 0.7304 0.7336 0.7067 0.7061 0.7142 0.7438 0.7308 0.7398 0.7317 0.7393 0.7328 0.7461 0.7545 0.7838 0.7446 0.739 0.7467 0.7557 0.7969 0.7315 0.7848 0.7345 0.7595 0.7348 0.7623 0.7653 0.761 0.7553 0.7725 0.7774 0.717 0.7338 0.7516 0.7538 0.7725 0.7617 0.7481 0.7928 0.8091 0.7585 0.748 0.7958 0.7465 0.7501 0.7324 -0.0743 -0.0705 -0.0551 -0.0666 -0.0658 -0.0652 -0.0562 -0.0648 -0.0592 -0.0589 -0.0501 -0.0505 -0.0639 -0.0551 -0.0659 -0.0607 -0.0562 -0.0613 -0.0611 -0.0633 -0.068 -0.0639 -0.0542 -0.0712 -0.0603 -0.0617 -0.0527 -0.0675 -0.0668 -0.0739 -0.057 -0.076 -0.0661 -0.0757 -0.0765 -0.0677 -0.0626 -0.0591 -0.0695 -0.0578 -0.0639 -0.0571 -0.0632 -0.0606 -0.0674 -0.0574 -0.0631 -0.064 -0.053 -0.0561 -0.0672 -0.0647 -0.0651
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2_110905531_C_T_b37 -0.212 110905530 C T ENSG00000144061.12_3 NPHP1 chr2 - 110905492 110905603 110904329 110904412 110907758 110907833 0.7758 0.7872 0.8415 0.7778 0.7993 0.7818 0.8017 0.8197 0.8343 0.8334 0.7182 0.7391 0.8373 0.8266 0.8341 0.8277 0.8253 0.8325 0.8105 0.8217 0.7844 0.7704 0.7626 0.7654 0.7512 0.784 0.8196 0.8025 0.8272 0.8127 0.7874 0.8274 0.8422 0.8438 0.8397 0.7695 0.8175 0.8042 0.756 0.6931 0.828 0.788 0.7918 0.8103 0.8211 0.7893 0.7903 0.8243 0.7273 0.7366 0.7346 0.7811 0.7928 -0.2073 -0.1943 -0.1897 -0.2048 -0.212 -0.209 -0.1955 -0.1662 -0.1572 -0.1486 -0.1576 -0.1693 -0.1381 -0.1415 -0.1568 -0.1523 -0.1498 -0.153 -0.1707 -0.1642 -0.2007 -0.1854 -0.1927 -0.1923 -0.1912 -0.19 -0.2038 -0.2005 -0.1971 -0.1906 -0.1882 -0.1879 -0.1752 -0.1708 -0.1885 -0.2108 -0.1822 -0.19 -0.2075 -0.1762 -0.1764 -0.1918 -0.2055 -0.1908 -0.1923 -0.1976 -0.1957 -0.1582 -0.1702 -0.2018 -0.1938 -0.1914 -0.1775
2_166854706_G_C_b37 -0.2885 166854705 G C ENSG00000144285.17_3 SCN1A chr2 - 166854547 166854685 166852522 166852627 166856232 166856286 0.7756 0.7837 0.7956 0.7727 0.7808 0.7448 0.7684 0.7681 0.7593 0.7895 0.7157 0.7424 0.7549 0.7605 0.7767 0.7552 0.7561 0.7932 0.7845 0.7785 0.7697 0.7724 0.6987 0.7309 0.7438 0.7766 0.8157 0.7922 0.8082 0.8148 0.7803 0.7766 0.7926 0.7959 0.7932 0.7706 0.8105 0.7811 0.7802 0.6806 0.7746 0.7571 0.7836 0.7491 0.7573 0.809 0.8099 0.7985 0.7039 0.7653 0.7369 0.7531 0.755 -0.2494 -0.2301 -0.2569 -0.2339 -0.2366 -0.2583 -0.2412 -0.2627 -0.2518 -0.2475 -0.1942 -0.2055 -0.2188 -0.2011 -0.2649 -0.2506 -0.2466 -0.256 -0.2514 -0.2591 -0.2451 -0.2643 -0.2471 -0.2258 -0.2459 -0.2298 -0.2545 -0.2503 -0.2443 -0.2402 -0.235 -0.2679 -0.2469 -0.2605 -0.2874 -0.2294 -0.2885 -0.245 -0.233 -0.2597 -0.2618 -0.2276 -0.2293 -0.2511 -0.2606 -0.2445 -0.214 -0.2662 -0.1909 -0.246 -0.239 -0.232 -0.2609
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5_112102045_G_T_b37 -0.4181 112102044 G T ENSG00000134982.16_3 APC chr5 + 112102022 112102107 112043218 112043579 112102885 112103087 0.9709 0.9738 0.9726 0.9705 0.972 0.9653 0.967 0.9728 0.9694 0.9718 0.9309 0.9372 0.9693 0.9648 0.9731 0.9709 0.9663 0.9743 0.9706 0.9751 0.9706 0.9678 0.9596 0.9692 0.9654 0.9688 0.9774 0.9743 0.9714 0.9756 0.9683 0.9768 0.9754 0.9796 0.9815 0.9696 0.9764 0.9724 0.9673 0.9623 0.9806 0.9637 0.9726 0.9702 0.9698 0.9755 0.9726 0.9798 0.9436 0.9678 0.9631 0.9674 0.9702 -0.3412 -0.3469 -0.3623 -0.3958 -0.3609 -0.3676 -0.3464 -0.3885 -0.3886 -0.3446 -0.3204 -0.3341 -0.3393 -0.349 -0.3744 -0.3651 -0.3539 -0.3542 -0.3318 -0.361 -0.3377 -0.3786 -0.4181 -0.348 -0.3531 -0.3412 -0.321 -0.3295 -0.3913 -0.3222 -0.3467 -0.3581 -0.3478 -0.3216 -0.2959 -0.3488 -0.3254 -0.3417 -0.3672 -0.3677 -0.3139 -0.274 -0.2868 -0.4018 -0.402 -0.3211 -0.3125 -0.33 -0.302 -0.3319 -0.3815 -0.3781 -0.4039
5_112102045_G_T_b37 -0.2126 112102044 G T ENSG00000134982.16_3 APC chr5 + 112102022 112102107 112090569 112090722 112102885 112103019 0.9809 0.9811 0.9827 0.9826 0.9835 0.9786 0.9762 0.9781 0.974 0.9769 0.9439 0.9507 0.9698 0.9672 0.9782 0.974 0.9727 0.9795 0.979 0.9788 0.9818 0.9815 0.973 0.9791 0.9767 0.9816 0.9835 0.9841 0.9851 0.9856 0.9778 0.984 0.9844 0.9829 0.9856 0.9802 0.9837 0.9832 0.9754 0.9763 0.9868 0.9757 0.9795 0.9815 0.982 0.98 0.9812 0.9852 0.9537 0.9772 0.9751 0.978 0.9816 -0.1638 -0.1756 -0.159 -0.1916 -0.1724 -0.1813 -0.1824 -0.189 -0.1869 -0.1736 -0.2126 -0.1878 -0.1656 -0.1678 -0.1763 -0.186 -0.1859 -0.1685 -0.1741 -0.1751 -0.1651 -0.1598 -0.2 -0.1958 -0.1757 -0.176 -0.1382 -0.1719 -0.1576 -0.1633 -0.1776 -0.1657 -0.1513 -0.1545 -0.1413 -0.1643 -0.1558 -0.1638 -0.197 -0.1722 -0.1311 -0.135 -0.157 -0.1768 -0.1767 -0.143 -0.149 -0.139 -0.1903 -0.1677 -0.2038 -0.1839 -0.1888
5_112102045_G_T_b37 -0.2117 112102044 G T ENSG00000134982.16_3 APC chr5 + 112102022 112102107 112090569 112090722 112102885 112103087 0.9817 0.9822 0.9837 0.9831 0.9838 0.9789 0.9771 0.9807 0.9765 0.9788 0.9427 0.9489 0.9731 0.9707 0.9804 0.9769 0.9751 0.9816 0.9808 0.9812 0.9824 0.9819 0.9728 0.9791 0.9767 0.9828 0.9845 0.9846 0.986 0.9856 0.9769 0.9847 0.9855 0.9856 0.9868 0.9807 0.9855 0.9839 0.9751 0.977 0.9878 0.9764 0.981 0.9826 0.9831 0.9813 0.9824 0.9867 0.9544 0.9775 0.9752 0.9798 0.9835 -0.1609 -0.1766 -0.17 -0.198 -0.177 -0.189 -0.1775 -0.1872 -0.1883 -0.1711 -0.2117 -0.1949 -0.1714 -0.1716 -0.1787 -0.1822 -0.1828 -0.1691 -0.1751 -0.173 -0.1645 -0.1642 -0.2044 -0.1988 -0.1757 -0.1758 -0.1408 -0.1755 -0.1552 -0.1612 -0.179 -0.1709 -0.1566 -0.1592 -0.147 -0.1711 -0.1531 -0.1676 -0.1983 -0.1704 -0.1303 -0.1391 -0.1577 -0.1739 -0.1753 -0.1531 -0.151 -0.14 -0.1914 -0.1727 -0.207 -0.1838 -0.1891
8_68066380_C_G_b37 -0.1084 68066379 C G ENSG00000104218.14_2 CSPP1 chr8 + 68066258 68066371 68049690 68049838 68070681 68070831 0.9041 0.9068 0.9213 0.9144 0.9158 0.8918 0.8998 0.9202 0.9176 0.9191 0.8221 0.8395 0.9101 0.9162 0.9192 0.925 0.917 0.9196 0.927 0.9285 0.9086 0.9115 0.8547 0.8959 0.8965 0.911 0.9277 0.9053 0.9221 0.909 0.8941 0.9274 0.9281 0.9237 0.9201 0.891 0.9226 0.9322 0.9016 0.8858 0.9264 0.8806 0.888 0.9084 0.9112 0.9204 0.9238 0.9277 0.8439 0.8981 0.8839 0.9072 0.8997 -0.0821 -0.0807 -0.0773 -0.0852 -0.0856 -0.0895 -0.0763 -0.0639 -0.0639 -0.0621 -0.0929 -0.0839 -0.0691 -0.0689 -0.0654 -0.0652 -0.0621 -0.0633 -0.0668 -0.0633 -0.0835 -0.0888 -0.104 -0.0843 -0.0872 -0.0889 -0.0746 -0.0892 -0.0715 -0.081 -0.0815 -0.0689 -0.073 -0.0756 -0.0763 -0.0914 -0.078 -0.0604 -0.0873 -0.0985 -0.0669 -0.0932 -0.1084 -0.0797 -0.0756 -0.074 -0.0744 -0.0722 -0.0894 -0.1035 -0.0849 -0.0807 -0.0915
8_68066380_C_G_b37 -0.0936 68066379 C G ENSG00000104218.14_2 CSPP1 chr8 + 68066258 68066371 68062017 68062170 68070681 68070831 0.9305 0.9361 0.9374 0.9379 0.9399 0.913 0.9241 0.9416 0.938 0.9406 0.8442 0.8618 0.9341 0.935 0.9387 0.9405 0.939 0.9413 0.9459 0.949 0.9336 0.9319 0.8876 0.9217 0.9207 0.9337 0.9469 0.9325 0.9438 0.9311 0.9222 0.9424 0.9406 0.944 0.9431 0.9188 0.938 0.9493 0.927 0.9059 0.9414 0.9006 0.9228 0.9262 0.9301 0.9421 0.9437 0.9459 0.8462 0.927 0.9111 0.929 0.9223 -0.0544 -0.0594 -0.0646 -0.0636 -0.0623 -0.0777 -0.0616 -0.0548 -0.0531 -0.0507 -0.0788 -0.071 -0.0572 -0.0545 -0.0551 -0.055 -0.0552 -0.0518 -0.0577 -0.0497 -0.0577 -0.0721 -0.0936 -0.0735 -0.0788 -0.0656 -0.0571 -0.0654 -0.0604 -0.0607 -0.0688 -0.0598 -0.0598 -0.062 -0.0628 -0.0734 -0.0645 -0.048 -0.0708 -0.0888 -0.0617 -0.0796 -0.0755 -0.0671 -0.06 -0.0601 -0.0571 -0.0585 -0.0841 -0.0774 -0.0804 -0.0617 -0.07
X_135112295_G_A_b37 -0.204 135112294 G A ENSG00000198689.10_3 SLC9A6 chrX + 135112290 135112321 135106488 135106642 135115572 135115652 0.3728 0.3847 0.4476 0.3724 0.3846 0.3672 0.4182 0.395 0.4288 0.4279 0.4523 0.4676 0.4551 0.4421 0.4042 0.4181 0.4253 0.4256 0.4192 0.4107 0.379 0.3501 0.3288 0.4004 0.409 0.3636 0.3831 0.3685 0.436 0.3686 0.4006 0.3767 0.4073 0.3809 0.4095 0.4009 0.3892 0.4539 0.4034 0.3834 0.4257 0.4419 0.4064 0.4353 0.4428 0.389 0.4388 0.4047 0.4071 0.3791 0.3663 0.4139 0.4068 -0.165 -0.1612 -0.1943 -0.1591 -0.1676 -0.1576 -0.1829 -0.1606 -0.166 -0.1652 -0.1451 -0.1606 -0.1693 -0.1643 -0.1616 -0.1612 -0.1629 -0.1698 -0.1565 -0.1651 -0.1628 -0.1512 -0.1402 -0.1571 -0.1669 -0.1513 -0.1736 -0.1589 -0.1695 -0.1539 -0.1582 -0.165 -0.1816 -0.1666 -0.1762 -0.1817 -0.1669 -0.1838 -0.1637 -0.1587 -0.1789 -0.1782 -0.1791 -0.2025 -0.204 -0.1759 -0.1752 -0.1734 -0.13 -0.1595 -0.1455 -0.1769 -0.1524
X_135112295_G_A_b37 -0.1874 135112294 G A ENSG00000198689.10_3 SLC9A6 chrX + 135112290 135112321 135106614 135106642 135122202 135122243 0.4019 0.4063 0.4462 0.3971 0.4093 0.4044 0.4355 0.4249 0.4569 0.4522 0.4109 0.4202 0.4648 0.4696 0.4319 0.4662 0.4618 0.454 0.4183 0.4378 0.4004 0.3547 0.3966 0.4029 0.4061 0.4101 0.4088 0.3907 0.4051 0.3837 0.4027 0.4222 0.4753 0.4189 0.4533 0.4103 0.4198 0.4674 0.3855 0.3607 0.4622 0.4246 0.4209 0.4237 0.422 0.4277 0.4451 0.4352 0.4392 0.3908 0.379 0.3912 0.4567 -0.1689 -0.1641 -0.164 -0.1631 -0.1659 -0.1644 -0.1619 -0.1491 -0.1483 -0.1389 -0.1301 -0.1291 -0.1526 -0.151 -0.1479 -0.142 -0.1395 -0.1527 -0.1435 -0.1511 -0.1654 -0.1486 -0.1564 -0.1556 -0.1504 -0.1477 -0.1597 -0.1489 -0.1583 -0.1445 -0.1479 -0.169 -0.1874 -0.1536 -0.1691 -0.1654 -0.1633 -0.1549 -0.1462 -0.1382 -0.1761 -0.144 -0.1565 -0.171 -0.1689 -0.1705 -0.1614 -0.1526 -0.1306 -0.1357 -0.1305 -0.1505 -0.1646
X_135112295_G_A_b37 -0.2126 135112294 G A ENSG00000198689.10_3 SLC9A6 chrX + 135112290 135112321 135111044 135111134 135115572 135115652 0.4691 0.4679 0.5036 0.4799 0.4977 0.4613 0.5023 0.461 0.4685 0.4854 0.4846 0.4866 0.4754 0.4802 0.4658 0.4721 0.4767 0.494 0.4983 0.4768 0.4639 0.403 0.3944 0.4843 0.4922 0.4727 0.4837 0.4567 0.5076 0.4619 0.4813 0.4689 0.4928 0.4758 0.5026 0.497 0.5046 0.4909 0.475 0.452 0.5321 0.4947 0.4895 0.512 0.5188 0.4956 0.5279 0.513 0.4663 0.4639 0.4572 0.476 0.518 -0.1959 -0.1926 -0.1996 -0.1833 -0.1953 -0.1698 -0.2009 -0.1777 -0.1801 -0.1761 -0.1348 -0.1451 -0.182 -0.1782 -0.1772 -0.1802 -0.1732 -0.1828 -0.1785 -0.1874 -0.189 -0.1707 -0.1622 -0.175 -0.1848 -0.1764 -0.2026 -0.1771 -0.1912 -0.1806 -0.1774 -0.1895 -0.207 -0.2051 -0.2037 -0.1998 -0.2035 -0.1921 -0.1905 -0.1669 -0.2066 -0.1786 -0.2047 -0.204 -0.2057 -0.2076 -0.2062 -0.2069 -0.1338 -0.1872 -0.1635 -0.1843 -0.2126
X_135112295_G_A_b37 -0.2213 135112294 G A ENSG00000198689.10_3 SLC9A6 chrX + 135112290 135112321 135111601 135112052 135115572 135115652 0.4547 0.4363 0.4738 0.4331 0.4556 0.4266 0.4892 0.4123 0.4389 0.4307 0.4776 0.5136 0.4659 0.4781 0.4143 0.425 0.4361 0.4301 0.4285 0.4188 0.4527 0.4236 0.408 0.4404 0.4545 0.4656 0.485 0.4518 0.5094 0.4539 0.4473 0.4284 0.4554 0.4314 0.4929 0.4588 0.4804 0.4532 0.4829 0.4585 0.5024 0.4871 0.4706 0.4943 0.51 0.4898 0.4967 0.4721 0.4887 0.4848 0.4524 0.4691 0.4673 -0.188 -0.1777 -0.1919 -0.1866 -0.1908 -0.168 -0.2022 -0.1473 -0.1552 -0.15 -0.1321 -0.1567 -0.1611 -0.1635 -0.1487 -0.1551 -0.1483 -0.1533 -0.1585 -0.1512 -0.1878 -0.1821 -0.1566 -0.1733 -0.168 -0.1769 -0.1987 -0.1829 -0.2149 -0.179 -0.1854 -0.1597 -0.1722 -0.1744 -0.1905 -0.1981 -0.2123 -0.1651 -0.1866 -0.1637 -0.1835 -0.1794 -0.1935 -0.2118 -0.2213 -0.2019 -0.1844 -0.1852 -0.1346 -0.1932 -0.1602 -0.1945 -0.1682

Predicting splicing levels of AS events

Option 1. User-provided AS events

  • The pre-compiled AS events and RBP expression levels across 53 GTEx tissues will be used for prediction.
  • iDARTS can make predictions for SE, A3SS, and A5SS. The format of each AS type can be found in rmats-turbo. More specifically:
    • Shared columns:
      • ID: rMATS event id
      • GeneID: Gene id
      • geneSymbol: Gene name
      • chr: Chromosome
      • strand: Strand of the gene
    • SE: exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
      • The inclusion form includes the target exon (exonStart_0base, exonEnd)
    • A3SS, A5SS: longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
      • The inclusion form includes the long exon (longExonStart_0base, longExonEnd) instead of the short exon (shortES shortEE)
  • Process the AS events and make predicts on the AS events
# Build sequence features for user-provided AS events
./bin/iDARTS build_feature -i ./example/example.SE_events.txt -t SE -o ./example/example.SE_events.feature
# Predict splicing levels based on the sequence features and RBP expression levels across 53 GTEx tissues
./bin/iDARTS predict -i ./example/example.SE_events.feature -o ./example/example.SE_events.PSI.txt

Option 2. User-provided AS events, and RBP expression levels for specific sample types of interest

  • The preparation of AS events can be found in the above Option 1.
  • iDARTS can make predictions for specific sample types of interest. This is enabled by preparing input gene expression file (TPM values quantified by Kallisto).
  • The format of gene expression file:
    • Column Name
      • GeneID: Gene id
      • Sample1,Sample2,Sample3,...: Expression levels of different samples separated by comma
  • Process the AS events and make predicts on the AS events
# Build sequence features for user-provided AS events
./bin/iDARTS build_feature -i ./example/example.SE_events.txt -t SE -o ./example/example.SE_events.feature
# Predict splicing levels based on the sequence features and user-provided RBP expression levels
./bin/iDARTS predict -i ./example/example.SE_events.feature -e ./example/example.RBP_expression_in_tissues.txt -o ./example/example.SE_events.PSI.txt

Output format:

iDARTS Prediction columns: (Suppose we have three samples with sample name Sample1, Sample2, and Sample3 specified in user-provided RBP expression levels of sample types. When not provided, the RBP expression levels across 53 GTEx tissues will be used.)

  • ID: AS event ID
  • Sample1: The predicted PSI of the target AS event in Sample1
  • Sample2: The predicted PSI of the target AS event in Sample2
  • Sample3: The predicted PSI of the target AS event in Sample3

Example output:

ID Adipose - Subcutaneous Adipose - Visceral (Omentum) Adrenal Gland Artery - Aorta Artery - Coronary Artery - Tibial Bladder Brain - Amygdala Brain - Anterior cingulate cortex (BA24) Brain - Caudate (basal ganglia) Brain - Cerebellar Hemisphere Brain - Cerebellum Brain - Cortex Brain - Frontal Cortex (BA9) Brain - Hippocampus Brain - Hypothalamus Brain - Nucleus accumbens (basal ganglia) Brain - Putamen (basal ganglia) Brain - Spinal cord (cervical c-1) Brain - Substantia nigra Breast - Mammary Tissue Cells - Cultured fibroblasts Cells - EBV-transformed lymphocytes Cervix - Ectocervix Cervix - Endocervix Colon - Sigmoid Colon - Transverse Esophagus - Gastroesophageal Junction Esophagus - Mucosa Esophagus - Muscularis Fallopian Tube Heart - Atrial Appendage Heart - Left Ventricle Kidney - Cortex Liver Lung Minor Salivary Gland Muscle - Skeletal Nerve - Tibial Ovary Pancreas Pituitary Prostate Skin - Not Sun Exposed (Suprapubic) Skin - Sun Exposed (Lower leg) Small Intestine - Terminal Ileum Spleen Stomach Testis Thyroid Uterus Vagina Whole Blood
1 0.84968394 0.8573682 0.85443765 0.82785386 0.8405348 0.83592635 0.8288909 0.8614947 0.8621079 0.86819685 0.82743853 0.82081664 0.84860134 0.86256295 0.86479187 0.8665389 0.8512182 0.8712268 0.84598494 0.86883926 0.85942906 0.8509599 0.87322223 0.8492014 0.8481797 0.8562976 0.8675173 0.8551014 0.8384222 0.84500504 0.84326905 0.8584442 0.8759451 0.85840636 0.88302743 0.8497585 0.860178 0.8509782 0.86537397 0.84920055 0.8792636 0.87121475 0.8462427 0.8576953 0.8551431 0.87143594 0.8930454 0.8750065 0.84019804 0.87396765 0.83557403 0.84311163 0.87467927
2 0.83895123 0.8343612 0.8298761 0.82199395 0.82192963 0.7968263 0.8307266 0.81800175 0.8170125 0.8207113 0.723578 0.75132906 0.8097334 0.8212083 0.8253972 0.81627834 0.8182904 0.8213665 0.8375982 0.8165619 0.8544024 0.78678966 0.8148767 0.8300732 0.80908716 0.8347909 0.8299305 0.8374791 0.8354722 0.8295299 0.8236433 0.80426395 0.797258 0.8216505 0.83364785 0.83438474 0.85284644 0.79705846 0.82240963 0.798681 0.8464341 0.83809835 0.8383695 0.8355557 0.8354534 0.83957136 0.84319717 0.8381713 0.76055014 0.802122 0.8142478 0.84807587 0.8320872
3 0.94990903 0.9500262 0.96086276 0.9507657 0.9527458 0.95124644 0.956538 0.9448721 0.93556434 0.9404098 0.912032 0.91218966 0.929809 0.92930955 0.94656116 0.93947124 0.932442 0.945741 0.9508486 0.9490776 0.9514591 0.9571419 0.9537283 0.9566221 0.94590634 0.9568837 0.9533268 0.955526 0.95586807 0.9550718 0.93325883 0.94532585 0.9507025 0.9527365 0.9576734 0.9438642 0.95000553 0.9386064 0.9389464 0.94185716 0.9584864 0.9386424 0.9522991 0.9454492 0.9452857 0.9541873 0.9587205 0.95456374 0.91552055 0.9440998 0.94690955 0.9511154 0.9538746
4 0.66383517 0.65358347 0.6856481 0.68188876 0.6772169 0.66304415 0.6897646 0.6025648 0.6256563 0.63855565 0.6032933 0.6459148 0.65917224 0.6277319 0.623116 0.61480093 0.6043807 0.65707874 0.64441454 0.63375884 0.658697 0.64484483 0.6045522 0.6537133 0.6441805 0.7078532 0.67487085 0.7006858 0.67629486 0.7179468 0.63680744 0.6377591 0.6413164 0.6335269 0.61699945 0.64880025 0.69777286 0.6294916 0.68338287 0.6118497 0.6382142 0.6253558 0.64951193 0.6339547 0.6476022 0.6448241 0.70647943 0.6524449 0.59490335 0.63531137 0.6318237 0.66594946 0.6322639
5 0.94516075 0.9504159 0.9496317 0.9448451 0.95014036 0.9351665 0.9348823 0.9194937 0.9188514 0.9230591 0.83977205 0.8668829 0.91940343 0.92177355 0.9202 0.9276293 0.9137637 0.9250215 0.9198702 0.9329916 0.93696296 0.9471179 0.91952944 0.9185726 0.91343766 0.9394409 0.947162 0.9448663 0.9406872 0.94791496 0.9130702 0.9509269 0.9482428 0.934765 0.94196546 0.93576896 0.9514066 0.94778633 0.91164625 0.8987833 0.9390998 0.91655445 0.9258796 0.93320656 0.9360073 0.9392521 0.93816245 0.94464225 0.85342246 0.90863895 0.90582675 0.92608005 0.92377627
6 0.9512707 0.95454043 0.955742 0.9509466 0.95545834 0.9426406 0.9433716 0.9250286 0.9265804 0.9293979 0.8528031 0.87790966 0.92361087 0.9263843 0.9267666 0.9331527 0.9211604 0.93254805 0.9293966 0.9384743 0.94264615 0.95481694 0.925292 0.92770493 0.9228808 0.94696915 0.95198935 0.9503826 0.94648916 0.9534141 0.92455167 0.95611095 0.9542403 0.94148815 0.9469306 0.9420104 0.9563278 0.9498618 0.9207492 0.90948343 0.9452934 0.925645 0.9316037 0.93772334 0.94243985 0.9443485 0.9427036 0.95033395 0.8643495 0.9175434 0.91594344 0.93442565 0.9318248
7 0.86397296 0.86746615 0.88374984 0.8767478 0.8800268 0.8612379 0.86078864 0.8503564 0.8532217 0.8569271 0.77435577 0.8022825 0.85560477 0.84525603 0.8560278 0.8616382 0.8405423 0.8638078 0.8611984 0.86927205 0.86064005 0.87236387 0.8129018 0.8445736 0.83713543 0.8635236 0.88073844 0.88153136 0.8741933 0.8876031 0.8349956 0.8973886 0.88783914 0.8679245 0.85794497 0.8613699 0.89624107 0.850076 0.8459414 0.7855401 0.8736121 0.8407768 0.8603221 0.8601667 0.86669654 0.86505556 0.8640528 0.8815363 0.7505361 0.8320877 0.82098305 0.85576594 0.82720774
8 0.74600905 0.7238932 0.7774273 0.7792994 0.77127254 0.74941194 0.7751236 0.70033807 0.7066802 0.7126911 0.6447074 0.675048 0.730209 0.7073987 0.71250427 0.6978596 0.6819447 0.7322815 0.7178582 0.7223314 0.7292094 0.7310871 0.6801197 0.73729926 0.70769775 0.7742132 0.74761355 0.77408016 0.72798043 0.78077316 0.73620236 0.7321458 0.74658024 0.7271059 0.7168058 0.7074397 0.7709116 0.7320959 0.7459578 0.65664136 0.7347919 0.6684944 0.7229661 0.725994 0.73587835 0.71881735 0.74708545 0.751377 0.63139814 0.6988515 0.703585 0.7633378 0.729386
9 0.74709934 0.7418573 0.8106197 0.7279986 0.75908184 0.709865 0.7806756 0.72347385 0.7304086 0.7335598 0.7067414 0.70608795 0.71420336 0.7438307 0.7307808 0.7398007 0.7317089 0.73930156 0.7328101 0.74611413 0.75448495 0.7838267 0.744593 0.7389941 0.7466906 0.75573 0.79689443 0.73152053 0.78475714 0.73449975 0.7595314 0.7348433 0.7623285 0.7653218 0.76102483 0.7553394 0.7725123 0.77740395 0.7170223 0.73376197 0.7515925 0.75378954 0.7725164 0.7617408 0.7481345 0.79279804 0.8090898 0.75854266 0.7479905 0.7958192 0.74646676 0.75011843 0.7324474
10 0.7325169 0.7080504 0.78723705 0.6927866 0.724087 0.6823088 0.7636376 0.6804254 0.6891089 0.70683295 0.6857985 0.70097464 0.68910104 0.7083628 0.6907978 0.7107412 0.7060549 0.70051146 0.711305 0.7176836 0.7421918 0.7534275 0.69515276 0.7134668 0.7321815 0.72020954 0.7546852 0.7156718 0.7724274 0.7142967 0.7385094 0.71836025 0.7495484 0.73850644 0.72979474 0.73349315 0.76750165 0.7552899 0.7004414 0.6698346 0.7029677 0.7272819 0.7639408 0.74366987 0.72868013 0.75230205 0.78755987 0.7385495 0.7169949 0.7675293 0.69565934 0.74751043 0.62931293
11 0.91407156 0.91713667 0.9357424 0.92579997 0.9258052 0.9212577 0.90470296 0.92696273 0.9263951 0.9297387 0.8626903 0.8779972 0.9305943 0.9281372 0.9290339 0.9294899 0.9236824 0.9344307 0.92099607 0.9299323 0.90234864 0.9279354 0.91649914 0.8953023 0.89273006 0.9175817 0.92772734 0.915983 0.9243611 0.9166576 0.89455557 0.94264156 0.94332045 0.9375571 0.9367256 0.9062926 0.9281821 0.9438356 0.89163953 0.8972319 0.93262804 0.9177275 0.8921747 0.89624226 0.897985 0.92451537 0.92157686 0.9414336 0.8664072 0.89876115 0.88473684 0.8866402 0.91779196
12 0.82760143 0.83204937 0.8628601 0.85160285 0.8464257 0.8278438 0.80785626 0.84114134 0.8377935 0.85546494 0.7551175 0.79684144 0.84988487 0.84654456 0.8503391 0.8466544 0.8501183 0.8578949 0.82693005 0.8406556 0.8149306 0.8062314 0.803034 0.81452596 0.79407865 0.83320224 0.8511246 0.83432657 0.8460727 0.83332765 0.7987151 0.86772156 0.8646943 0.8662308 0.8568735 0.83144313 0.86123 0.8575916 0.80087644 0.7647201 0.8436778 0.8258563 0.8057254 0.7975041 0.7947777 0.83943 0.81594944 0.86224926 0.7273362 0.7880707 0.7760471 0.80509645 0.8172555
13 0.83343667 0.84021556 0.8740217 0.85634327 0.85351974 0.83678436 0.81808585 0.84820193 0.8443076 0.85778904 0.7790885 0.81153905 0.85909426 0.8536908 0.8534508 0.85632706 0.8535069 0.85966986 0.834246 0.8465274 0.8195283 0.8235539 0.818864 0.81656426 0.80857974 0.84475964 0.8580844 0.8466347 0.8570935 0.84520996 0.80956924 0.8723469 0.8734846 0.87273407 0.85818243 0.8417667 0.8688307 0.86123484 0.81050795 0.78973687 0.8487048 0.83948994 0.81372976 0.8112408 0.8109148 0.8496871 0.82846785 0.8692179 0.74443144 0.80300504 0.7866528 0.8022906 0.81492186
14 0.9073515 0.9103961 0.92607516 0.92117244 0.92160785 0.9155405 0.8985611 0.92246485 0.9224347 0.92599773 0.85449755 0.8697812 0.926483 0.924438 0.925282 0.9265674 0.9198723 0.9294472 0.9146288 0.92379105 0.8964437 0.92415774 0.9052393 0.89159214 0.8880688 0.9130802 0.91986674 0.9116934 0.9164133 0.9119917 0.88878953 0.9365697 0.93796223 0.9281284 0.9308816 0.9030093 0.920266 0.93733597 0.8863055 0.88585204 0.92646617 0.90966356 0.88793886 0.8884543 0.89060724 0.91642106 0.9109786 0.93313277 0.85545814 0.8938258 0.8803527 0.88123685 0.90915823
15 0.90923786 0.91065466 0.9265529 0.9207506 0.9204068 0.9182707 0.8988161 0.9234947 0.92260045 0.9265722 0.85485303 0.8721196 0.9287211 0.9261864 0.92614716 0.9278886 0.92017955 0.9299387 0.9168146 0.9256257 0.89779395 0.924808 0.9090807 0.89117205 0.8875772 0.91303426 0.9187926 0.912028 0.91752416 0.91270435 0.8879217 0.9372218 0.9386894 0.92829084 0.9292076 0.9023737 0.91949254 0.9395277 0.8863737 0.88572294 0.92507803 0.90831614 0.8898918 0.8887812 0.8905368 0.91579455 0.91033334 0.9329545 0.8580456 0.8908783 0.8798951 0.8810487 0.909427
16 0.8602273 0.8583001 0.8797926 0.86827964 0.8752721 0.86599255 0.84968436 0.8725716 0.8786241 0.87942964 0.76478237 0.8008796 0.8782212 0.8760465 0.87741363 0.8765494 0.8766171 0.88206637 0.853994 0.87459373 0.8399364 0.86656 0.84651196 0.80821973 0.80971134 0.858527 0.8739873 0.85354817 0.86425275 0.86125135 0.8247094 0.8734511 0.8829136 0.8647051 0.8752306 0.8534626 0.87700593 0.88156354 0.84580934 0.79319394 0.87750614 0.84769714 0.8395311 0.8277601 0.836119 0.87667716 0.8671384 0.88546866 0.784528 0.829875 0.8024996 0.8244095 0.84125817
17 0.89859694 0.89795923 0.916214 0.9094664 0.91197854 0.90983903 0.891013 0.91122496 0.9132098 0.91506803 0.84498703 0.85650903 0.9179428 0.9172953 0.9149941 0.9181547 0.9091576 0.91755295 0.9034201 0.9125822 0.88698924 0.91843903 0.8932158 0.88664496 0.8819984 0.9058201 0.9062309 0.90327185 0.90001327 0.90421325 0.88334846 0.9248203 0.92612106 0.9145051 0.92292196 0.89466774 0.90725935 0.92443764 0.8798872 0.87042445 0.9170413 0.9016773 0.8813025 0.87277937 0.87573355 0.9031371 0.8980996 0.9164313 0.84511757 0.8821065 0.876787 0.86872137 0.89067566
18 0.90128195 0.89974976 0.9163455 0.91082513 0.9127563 0.91407144 0.89269793 0.91504127 0.9162118 0.91808254 0.8474339 0.8613331 0.9217826 0.92023593 0.91771823 0.9215518 0.9122571 0.91954404 0.9087303 0.9170617 0.89009917 0.91764194 0.900092 0.8857821 0.882109 0.90713674 0.9053521 0.9043385 0.90478194 0.90636647 0.8830474 0.9269101 0.9268697 0.91549903 0.92217904 0.89549094 0.9060098 0.93030584 0.87867785 0.8724238 0.9143793 0.9006112 0.8822645 0.8755104 0.8772758 0.90311784 0.8970152 0.9184691 0.85019815 0.87986195 0.8777112 0.8713827 0.89186126
19 0.5148861 0.4838584 0.5241456 0.51845473 0.4904287 0.49661547 0.52218145 0.4668033 0.47564015 0.49286398 0.50819784 0.5628712 0.50135964 0.48381543 0.46464968 0.45198423 0.48767385 0.48941964 0.46439314 0.47637957 0.5003433 0.40299258 0.47041106 0.5115839 0.5068773 0.46910176 0.46826062 0.4578019 0.52419436 0.45541826 0.5266739 0.47750005 0.4974044 0.49718517 0.5065816 0.52356845 0.5070601 0.47708526 0.5373729 0.5202588 0.5242063 0.57200444 0.526701 0.49444056 0.4886077 0.5066331 0.5319418 0.51575613 0.4835156 0.55610806 0.4582719 0.48316178 0.44541487
20 0.83246815 0.8220504 0.85688514 0.84707963 0.85047656 0.82843083 0.82732993 0.81118757 0.8202332 0.82369053 0.76004976 0.80066645 0.8229685 0.8129635 0.8122606 0.8088685 0.81200254 0.82062566 0.8121486 0.8189365 0.82527226 0.80756533 0.8298448 0.83003634 0.8169193 0.8328595 0.8335435 0.84027576 0.8517395 0.8373976 0.81677246 0.81726485 0.83186454 0.8384017 0.82542115 0.834849 0.8543849 0.827336 0.8107222 0.8065051 0.8251623 0.841436 0.845122 0.8081605 0.82364637 0.8481552 0.84596634 0.8436537 0.7575201 0.83395845 0.8003419 0.83060914 0.81943476
21 0.93237484 0.93161935 0.94380283 0.9413832 0.93824065 0.9315014 0.94044226 0.9172242 0.91929924 0.9189434 0.87254846 0.88190764 0.90589523 0.90886575 0.9173559 0.9228865 0.9112426 0.922983 0.927125 0.9273774 0.9306048 0.93329716 0.93031776 0.9283554 0.9276662 0.9302908 0.9435089 0.937774 0.94533396 0.93875456 0.9251503 0.9335715 0.9375416 0.94229364 0.9340962 0.9353548 0.94764835 0.93291634 0.9243271 0.9136669 0.94678676 0.9223601 0.9407562 0.931266 0.9334772 0.9404181 0.9403165 0.94730675 0.8844078 0.9354614 0.91487855 0.9343748 0.927917
22 0.928537 0.9245998 0.9322461 0.9370645 0.9320175 0.9285679 0.94019425 0.901313 0.8954921 0.8992651 0.8702776 0.88328934 0.88265455 0.8904606 0.9014336 0.9048706 0.89053124 0.90569985 0.90964776 0.9148289 0.92297727 0.9302785 0.931296 0.9286455 0.9294113 0.9308885 0.94530755 0.93284166 0.93541497 0.9335186 0.91981345 0.924277 0.92908776 0.93391705 0.9265779 0.9276354 0.9493076 0.92359704 0.9220603 0.91484624 0.93902606 0.91986054 0.93058664 0.92746526 0.9281828 0.94167244 0.93956643 0.9404 0.88879144 0.93194485 0.9219629 0.93191546 0.924389
23 0.9283637 0.92405206 0.9320523 0.9371664 0.9317872 0.9290888 0.9400579 0.90054196 0.8947786 0.8988401 0.8704626 0.8830897 0.88172865 0.89016134 0.9010991 0.90402997 0.8902402 0.9051124 0.90958196 0.91440564 0.92319536 0.93074065 0.9319048 0.92853296 0.92977536 0.9308527 0.94520205 0.93295443 0.9347412 0.93338776 0.91996825 0.9237623 0.928755 0.93365943 0.9257433 0.9271186 0.9487368 0.92406005 0.9232441 0.91486055 0.9383974 0.9197427 0.93080837 0.9274827 0.92795163 0.9411294 0.93934214 0.93972206 0.88889253 0.9320772 0.9223173 0.9316037 0.9240077
24 0.9229984 0.9248651 0.9288824 0.93193805 0.92742187 0.92679006 0.93519706 0.8991693 0.8993284 0.9018758 0.8660077 0.8770809 0.8844 0.8912414 0.9014284 0.9037474 0.8908683 0.90938884 0.9121523 0.91397554 0.9193457 0.92428046 0.9218782 0.92255306 0.927071 0.9269155 0.94179046 0.93130624 0.934523 0.93172264 0.91473186 0.9251665 0.92952883 0.9331131 0.9258736 0.92415965 0.9457911 0.9279497 0.9217973 0.90905046 0.93912286 0.91771966 0.9265585 0.9234087 0.9245659 0.9403642 0.93894976 0.93924934 0.8757825 0.929661 0.9136151 0.92598534 0.9250633
25 0.926321 0.92526835 0.9279283 0.9353447 0.9316429 0.928747 0.94068575 0.9022722 0.900321 0.9038242 0.8701943 0.87931806 0.8850271 0.8891328 0.9046224 0.9064411 0.8924324 0.9097969 0.9139665 0.91717976 0.92256916 0.93007296 0.9246637 0.92655504 0.9299843 0.93003243 0.94267416 0.93301994 0.93625754 0.93347263 0.9201044 0.9240898 0.92949665 0.93412846 0.9263752 0.9264287 0.9463023 0.92760956 0.9229372 0.9135138 0.9407762 0.919462 0.9273659 0.9249004 0.9262619 0.9418845 0.94115144 0.93945295 0.8808873 0.93068266 0.9190588 0.92791873 0.9263468
26 0.92093784 0.9130548 0.9119048 0.92865163 0.9220151 0.91959846 0.9333476 0.8967762 0.8879358 0.8993397 0.8618177 0.874276 0.87191504 0.877127 0.8988155 0.89607847 0.8869227 0.90598613 0.91079676 0.91087186 0.9166958 0.9244316 0.9210121 0.9181078 0.9221287 0.9259672 0.9396801 0.9282443 0.92481375 0.92617273 0.90916187 0.91723526 0.92062485 0.92087764 0.91126204 0.91742027 0.9397605 0.9114583 0.91763246 0.8980342 0.93011653 0.90392935 0.91698706 0.9178637 0.9204372 0.93857783 0.9350878 0.9335062 0.880074 0.91502225 0.913771 0.92251456 0.91272783
27 0.9360441 0.93754387 0.9378196 0.93059856 0.93400544 0.92073405 0.93008024 0.90754044 0.90150464 0.9104866 0.85097444 0.8648588 0.88763 0.88124293 0.90646374 0.89415234 0.89694005 0.9190024 0.9111303 0.9124007 0.9342758 0.9157637 0.91229045 0.91819745 0.91974485 0.9281826 0.9429575 0.9354464 0.9459235 0.9353344 0.9228759 0.929505 0.9320841 0.94114816 0.93589705 0.93418884 0.94922334 0.9220665 0.9259375 0.91102326 0.9435218 0.9275807 0.9395231 0.9378897 0.94035035 0.94557846 0.9434717 0.95079076 0.86401594 0.943103 0.90950954 0.93546736 0.93597066
28 0.775777 0.78724563 0.8414637 0.7778126 0.79933417 0.7817564 0.8016636 0.8197063 0.8342703 0.8333728 0.7181636 0.73910725 0.8372518 0.8266317 0.83413374 0.82771146 0.82529974 0.832466 0.8104701 0.82174903 0.7843789 0.770418 0.762564 0.76538426 0.7512001 0.78398 0.8196338 0.8024616 0.82721615 0.8127287 0.7873874 0.8274334 0.8421814 0.8438142 0.83970296 0.76954013 0.81748027 0.8042429 0.7560166 0.6930539 0.8279761 0.7880165 0.7917965 0.8102954 0.8210645 0.7893211 0.7902684 0.8243229 0.72726405 0.7365767 0.7345691 0.7811078 0.7928408
29 0.7755911 0.78365535 0.7955662 0.7726702 0.78081405 0.7447791 0.76837456 0.76806813 0.7593347 0.78946817 0.71571994 0.7423885 0.75488675 0.76050484 0.7767417 0.75515807 0.7560926 0.79323375 0.7844582 0.7785039 0.76967335 0.7723901 0.6986845 0.73087585 0.7438265 0.77657557 0.81567764 0.7922081 0.8082425 0.81479293 0.78027135 0.77660686 0.792617 0.7959313 0.7931905 0.77055144 0.8104944 0.7810618 0.78024703 0.6806043 0.77464974 0.75711787 0.7836178 0.7490552 0.75727844 0.8089902 0.809889 0.7984759 0.70388234 0.7652801 0.73691046 0.7531263 0.7549575
30 0.86907303 0.87709534 0.8892682 0.87890136 0.8797976 0.8652977 0.86624134 0.8751129 0.8729046 0.8730911 0.7953715 0.8016896 0.86001766 0.8556253 0.87606984 0.8513564 0.8616775 0.87776357 0.8659916 0.8667097 0.85733044 0.8636133 0.86460906 0.84825706 0.86301917 0.87906754 0.9028522 0.8837965 0.90144175 0.890666 0.8819518 0.8645133 0.8685664 0.884997 0.86303884 0.8631667 0.8997812 0.8736907 0.8517563 0.82723045 0.8892733 0.848231 0.88322103 0.8802334 0.8852254 0.89971745 0.89269936 0.8960395 0.83525074 0.8867612 0.86124974 0.8613554 0.87867373
31 0.97092545 0.9738407 0.9726168 0.9705167 0.9719955 0.96529067 0.967004 0.97283256 0.96943796 0.9717625 0.9308685 0.937183 0.9692934 0.9647868 0.973098 0.97087 0.9663455 0.9743085 0.9705864 0.97507733 0.9705836 0.9678353 0.95958966 0.969169 0.9653621 0.96882117 0.97737944 0.97429246 0.9713813 0.97563934 0.96830285 0.97678024 0.9754341 0.97956944 0.98149365 0.96961844 0.97641927 0.97243583 0.9672562 0.9622671 0.98063356 0.96369827 0.9725809 0.9701904 0.9697736 0.9755146 0.9726264 0.9798109 0.9435636 0.96781576 0.9630855 0.9674386 0.97016114
32 0.9809187 0.98109424 0.98273295 0.9826487 0.98353195 0.978567 0.9761998 0.97807217 0.97395384 0.97686213 0.9439065 0.9506919 0.9697952 0.96719944 0.9782325 0.9739771 0.97268903 0.9795052 0.9789502 0.97876567 0.9817687 0.98147506 0.97299594 0.9791468 0.9767038 0.98164785 0.9834835 0.98407555 0.98510504 0.9855609 0.9778174 0.98395765 0.98436326 0.9828917 0.9856383 0.9801574 0.9837014 0.9831983 0.9754168 0.9763497 0.9868142 0.97566974 0.97952974 0.98152065 0.98201495 0.98002803 0.98117673 0.9851729 0.95371073 0.9772339 0.9751421 0.9780224 0.9816267
33 0.9817122 0.98215216 0.98367465 0.9831109 0.9838104 0.97890437 0.9771002 0.9806876 0.9764554 0.9787552 0.9427277 0.9489355 0.9730997 0.97066057 0.98043 0.97687304 0.9751271 0.9816497 0.98083484 0.9812145 0.9823661 0.9819382 0.9727868 0.9791126 0.97674626 0.9827916 0.98450166 0.9845502 0.98600876 0.9856249 0.9768685 0.9847182 0.9854747 0.98561704 0.98682106 0.98074085 0.9854784 0.98394763 0.9750999 0.97697955 0.98784864 0.9763883 0.9809701 0.9825989 0.9831155 0.9813431 0.9823836 0.9866927 0.9544281 0.97746074 0.9751999 0.97978556 0.9834778
34 0.90410125 0.90680903 0.92128646 0.9143958 0.9158481 0.8918082 0.8997816 0.92019033 0.9175846 0.9191364 0.8220949 0.8395492 0.9100908 0.9162499 0.91915 0.9249789 0.91704196 0.9196264 0.9270242 0.9284948 0.90855324 0.9115389 0.85471135 0.8958686 0.8965312 0.91096485 0.92774934 0.90534735 0.9221341 0.9090401 0.8941072 0.9274341 0.92812806 0.92374074 0.9201213 0.8910345 0.9225856 0.9322237 0.9016053 0.8857511 0.92636603 0.8806467 0.8879943 0.9083681 0.91117775 0.9204297 0.9237857 0.92766094 0.8438548 0.8981447 0.88393563 0.9071585 0.89974517
35 0.9304651 0.9360754 0.9373642 0.9378651 0.9399136 0.91301155 0.9241265 0.9416006 0.9379646 0.9405562 0.84415454 0.86180687 0.9340555 0.93504936 0.93873155 0.94054794 0.9390136 0.9413017 0.9458993 0.9490113 0.93361175 0.9318949 0.887578 0.9217321 0.92073584 0.93365145 0.9469075 0.9325186 0.943766 0.9310853 0.9221939 0.94243354 0.9405548 0.9440449 0.9430636 0.9187519 0.9380477 0.9493167 0.9269924 0.9058603 0.9413884 0.90062684 0.9228462 0.9262284 0.9300885 0.9420837 0.94374263 0.9459003 0.8462122 0.92697465 0.91107005 0.92900574 0.9222956
36 0.37276235 0.38472813 0.44760126 0.372362 0.38463253 0.36715278 0.41816115 0.3950319 0.42877498 0.42786813 0.45232335 0.4676345 0.455053 0.4421401 0.40422136 0.41810757 0.42532867 0.42556134 0.41921002 0.41067284 0.37895823 0.35006508 0.3288232 0.40037045 0.40899235 0.36357552 0.38310692 0.36846977 0.43599766 0.36855298 0.40057832 0.37671006 0.4072884 0.38091877 0.4095339 0.40090442 0.38924876 0.45389405 0.40337506 0.38338327 0.42574772 0.44194323 0.40642586 0.43526858 0.44279003 0.3890094 0.4387764 0.40467644 0.40713868 0.37914062 0.36626363 0.41394567 0.4068156
37 0.40191346 0.40634757 0.44615278 0.39705473 0.4092539 0.4044037 0.43552646 0.42489815 0.45685062 0.45217052 0.41091973 0.42020637 0.46475536 0.46956053 0.43186265 0.4662307 0.4618371 0.45404863 0.41826898 0.43780708 0.40042695 0.3546711 0.3965548 0.40292516 0.40608087 0.41005453 0.40883064 0.39074016 0.40505153 0.38369936 0.4026986 0.42218208 0.47533503 0.4188973 0.45330304 0.4102736 0.4197692 0.46742886 0.3854998 0.3606917 0.46222892 0.42464933 0.42086166 0.42368037 0.422007 0.42772847 0.44507942 0.43524036 0.43923074 0.39076346 0.3789634 0.39115542 0.45674348
38 0.4691376 0.4679319 0.50362694 0.47989312 0.49773568 0.461327 0.50234014 0.46101514 0.46848312 0.48544127 0.48462301 0.48663735 0.47539192 0.4801535 0.46579772 0.4721485 0.47672677 0.493955 0.49828824 0.476755 0.4638551 0.40302858 0.39435464 0.48433357 0.4921872 0.47265634 0.48374778 0.45667648 0.50758064 0.46194023 0.48125058 0.4688631 0.49279913 0.475803 0.5026374 0.4970335 0.50455296 0.49088073 0.4750162 0.45198908 0.532062 0.49467832 0.48948687 0.5120142 0.5187799 0.4955965 0.5278772 0.51299065 0.46633315 0.4638737 0.45721117 0.47595787 0.5179861
39 0.45469823 0.43628588 0.47376496 0.4331115 0.45563206 0.4266189 0.48917022 0.4123408 0.4388849 0.430713 0.477571 0.5136075 0.46588764 0.47805786 0.41425338 0.4249959 0.43607974 0.4300545 0.4285265 0.41880354 0.45265284 0.42361134 0.4080407 0.44041795 0.45451146 0.4655818 0.48498982 0.45182982 0.50939286 0.45392948 0.44727486 0.4284223 0.4554248 0.43139118 0.49287686 0.4588147 0.48043832 0.45319575 0.4829255 0.45853528 0.5024455 0.48712936 0.47057968 0.49425825 0.50995857 0.4897833 0.49672437 0.47205067 0.4887423 0.48481122 0.45244223 0.46911916 0.4672882

Detailed arguments:

usage: iDARTS [-h] [--version]
              {get_resources,parse_vcf,build_feature,predict} ...

iDARTS - individualized Deep-learning Analysis of RNA Transcript Splicing

positional arguments:
  {get_resources,parse_vcf,build_feature,predict}
    get_resources       iDARTS get_resources: download hg19 fasta and
                        phastCons scores

    parse_vcf           iDARTS parse_vcf: get the predicted PSI values of
                        reference and alternative alleles as well as the
                        predicted deltaPSI in GTEx tissues or user-provided
                        RBP expression levels from the pre-compiled
                        alternative splicing events or user-provided events

    build_feature       iDARTS build_feature: build cis-sequence features for
                        alternative splicing events

    predict             iDARTS predict: predict PSI values given alternative
                        splicing events with annotated cis-sequence features
                        and RBP expression levels from the GTEx or user-
                        provided RBP expression levels

get_resources
  usage: iDARTS get_resources [-h] [-o OUT_DIR] [-f {True,False}]

  optional arguments:
    -h, --help            show this help message and exit
    -o OUT_DIR, --out-dir OUT_DIR
                          Optional, default user home directory: Output folder
                          for downloaded data
    -f {True,False}, --force {True,False}
                          Optional, force redownload of resources

parse_vcf
  usage: iDARTS parse_vcf [-h] [-t {SE,A5SS,A3SS}] [-i INPUT] -v VCF_PATH
                          [-e EXPR] -o OUTFILENAMEPREFIX  

  optional arguments:
    -h, --help            show this help message and exit
    -t {SE,A5SS,A3SS}, --type {SE,A5SS,A3SS}
                          Optional, default SE: specify the alternative splicing
                          event type. SE: skipped exons, A3SS: alternative 3
                          splice sites, A5SS: alternative 5 splice sites
    -i INPUT, --input INPUT
                          Optional, a list of alternative splicing events; If
                          not provided, the alternative splicing events will be
                          the pre-compiled events from GENCODEv26lift37
    -v VCF_PATH, --vcf_path VCF_PATH
                          the file location of the VCF
    -e EXPR, --expression EXPR
                          Optional, a list of RBP expression levels (TPM values
                          from Kallisto); header format
                          'Gene_ID\tExp1,Exp2,Exp3...(different expression
                          profiles separated by comma). If not provided, the
                          pre-compiled RBP expression levels from the GTEx will
                          be used.'
    -o OUTFILENAMEPREFIX, --outFileNamePrefix OUTFILENAMEPREFIX
                          output files name prefix (including full or relative
                          path).

build_feature
  usage: iDARTS build_feature [-h] [-t {SE,A5SS,A3SS}] -i INPUT
                              [-m {True,False}] -o OUTPUT

  optional arguments:
    -h, --help            show this help message and exit
    -t {SE,A5SS,A3SS}, --type {SE,A5SS,A3SS}
                          Optional, default SE: specify the alternative splicing
                          event type. SE: skipped exons, A3SS: alternative
                          3-prime splice sites, A5SS: alternative 5-prime splice
                          sites
    -i INPUT, --input INPUT
                          A list of alternative splicing events
    -m {True,False}, --mutate {True,False}
                          Whether annotate the sequence features with SNV (300nt
                          in the vicinity of skipped exons);
    -o OUTPUT, --out-file-name OUTPUT
                          Annotation output file name

predict
  usage: iDARTS predict [-h] [-t {SE,A5SS,A3SS}] -i INPUT [-e EXPR] -o OUTPUT

  optional arguments:
    -h, --help            show this help message and exit
    -t {SE,A5SS,A3SS}, --type {SE,A5SS,A3SS}
                          Optional, default SE: specify the alternative splicing
                          event type. SE: skipped exons, A3SS: alternative 3
                          splice sites, A5SS: alternative 5 splice sites
    -i INPUT, --input INPUT
                          A list of alternative splicing events with built cis-
                          sequence features; the input is the output of the
                          build_feature step
    -e EXPR, --expression EXPR
                          Optional, a list of RBP expression levels (TPM values
                          from Kallisto); header format
                          'Gene_ID\tExp1,Exp2,Exp3...(different expression
                          profiles separated by comma). If not provided, the
                          pre-compiled RBP expression levels from the GTEx will
                          be used.'
    -o OUTPUT, --out-file-name OUTPUT
                          The predicted PSI values for the alternative splicing
                          events

Contact

Mailing List / Group

GitHub Issues

Zhicheng Pan zcpan1016@gmail.com

Yi Xing xingyi@chop.edu

Copyright and License Information

Copyright (C) 2021 The Children’s Hospital of Philadelphia

Authors: Zhicheng Pan and Yi Xing

This program is licensed with commercial restriction use license. Please see the attached LICENSE file for details.

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Predicting splicing effects of human genome variants from sequences

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