EN-CODEC Supplementary Data

An integrative ENCODE resource for cancer: interpreting non-coding mutations and gene regulation
Supplementary Data

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EN-CODEC.DATA


Summary of EN-CODEC experiments

List of all EN-CODEC experiments (inc. external data)EC-001-MET.encodec_all_experiments.csv
TF ChIP-seq data summary (Oct 2017 freeze)EC-001-MET.encodec_Oct17_TF_ChIP-seq_data.csv
Deduplicated ChIP-seq list (Oct 2017 freeze)EC-001-MET.encodec_Oct17_deduplicated_ChIP-seq_list.csv
Decuplicated ChIP-seq matrix (Oct 2017 freeze)EC-001-MET.encodec_Oct17_deduplicated_ChIP-seq_matrix.csv
ENCODE key cell line ChIP-seq summaryEC-001-MET.encode_key_cell_line_ChIP-seq_data.csv

Expression and variant calls

Normalized cancer patient expression dataEC-001-COH.TCGA_data_2016_01_28.tar.gz
LIHC GermlineAvailable soon
LIHC SomaticAvailable soon

EN-CODEC.ANNOTATION


ENCODE cancer annotations

ENCODE cancer cell type summaryEC-002-MET.encode_cancer_cell_type_summary.csv
ENCODE cancer cell line summaryEC-002-MET.encode_cancer_cell_line_summary.csv

TF and RBP annotations

K562 vs GM12878 common TF classificationEC-002-MET.encodec_KG_common_TF_class.csv
K562 vs GM12878 common TF summaryEC-002-MET.encodec_KG_common_TF_summary.csv

Extended genes

HepG2 extended gene definitionEC-002-EXT.merge.post.extendedGene.HepG2.txt
K562 extended gene definitionEC-002-EXT.merge.post.extendedGene.K562.txt
MCF-7 extended gene definitionEC-002-EXT.merge.post.extendedGene.MCF-7.txt

EN-CODEC.ANALYSIS


MatchedFilter enhancer calls, SVM filtered

GM12878 MatchedFilter enhancersEC-003-CRE.MatchedFilter_GM12878.bed
GM12878 MatchedFilter enhancers mergedEC-003-CRE.MatchedFilter-merged_GM12878.bed
HepG2 MatchedFilter enhancersEC-003-CRE.MatchedFilter_HepG2.bed
HepG2 MatchedFilter enhancers mergedEC-003-CRE.MatchedFilter-merged_HepG2.bed
K562 MatchedFilter enhancersEC-003-CRE.MatchedFilter_K562.bed
K562 MatchedFilter enhancers mergedEC-003-CRE.MatchedFilter-merged_K562.bed
MCF-7 MatchedFilter enhancersEC-003-CRE.MatchedFilter_MCF-7.bed
MCF-7 MatchedFilter enhancers mergedEC-003-CRE.MatchedFilter-merged_MCF-7.bed
A549 MatchedFilter enhancersEC-003-CRE.MatchedFilter_A549.bed
A549 MatchedFilter enhancers mergedEC-003-CRE.MatchedFilter-merged_A549.bed
HeLa-S3 MatchedFilter enhancersAvailable soon
HeLa-S3 MatchedFilter enhancers mergedAvailable soon
H1-hESC MatchedFilter enhancersAvailable soon
H1-hESC MatchedFilter enhancers mergedAvailable soon

ESCAPE enhancer peak calls

GM12878 ESCAPE peak calls (raw)Available soon
K562 ESCAPE peak calls (raw)Available soon
MCF-7 ESCAPE peak calls (raw)EC-003-CRE.ESCAPE_MCF-7.bed
LNCaP ESCAPE peak calls (raw)EC-003-CRE.ESCAPE_LNCaP.bed
GM12878 ESCAPE peak calls (lenient, FC > 1.2)Available soon
K562 ESCAPE peak calls (lenient, FC > 1.2)Available soon
MCF-7 ESCAPE peak calls (lenient, FC > 1.2)EC-003-CRE.ESCAPE_MCF-7_lenient.bed
LNCaP ESCAPE peak calls (lenient, FC > 1.2)EC-003-CRE.ESCAPE_LNCaP_lenient.bed
GM12878 ESCAPE peak calls (strict, FC > 2)Available soon
K562 ESCAPE peak calls (strict, FC > 2)Available soon
MCF-7 ESCAPE peak calls (strict, FC > 2)EC-003-CRE.ESCAPE_MCF-7_strict.bed
LNCaP ESCAPE peak calls (strict, FC > 2)EC-003-CRE.ESCAPE_LNCaP_strict.bed

JEME enhancer target predictions

GM12878 JEME enhancer target gene predictionEC-003-CRE.JEME_of_MatchedFilter_GM12878.bed
HepG2 JEME enhancer target gene predictionEC-003-CRE.JEME_of_MatchedFilter_HepG2.bed
K562 JEME enhancer target gene predictionEC-003-CRE.JEME_of_MatchedFilter_K562.bed
MCF-7 JEME enhancer target gene predictionEC-003-CRE.JEME_of_MatchedFilter_MCF-7.bed
A549 JEME enhancer target gene predictionAvailable soon
HeLa-S3 JEME enhancer target gene predictionAvailable soon
H1-hESC JEME enhancer target gene predictionAvailable soon

Integrative enhancer annotations with accession to the Encyclopedia cRE

GM12878 MatchedFilterxESCAPE integrated annotation (with mapping to cRE accession)EC-003-CRE.MatchedFilterxESCAPE_GM12878.bed
K562 MatchedFilterxESCAPE integrated annotation (with mapping to cRE accession)EC-003-CRE.MatchedFilterxESCAPE_K562.bed
GM12878 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotationEC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_GM12878.bed
K562 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotationEC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_K562.bed
GM12878 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotation, Hi-C annotated (last col)EC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_FitHiC_GM12878.bed
K562 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotation, Hi-C annotated (last col)EC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_FitHiC_K562.bed
GM12878 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotation, Hi-C annotated, mergedEC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_FitHiC_GM12878_merged.bed
K562 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotation, Hi-C annotated, mergedEC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_FitHiC_K562_merged.bed
GM12878 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotation, Hi-C filtered (q-val<0.1)EC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_FitHiC-filtered_GM12878.bed
K562 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotation, Hi-C filtered (q-val<0.1)EC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_FitHiC-filtered_K562.bed
GM12878 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotation, Hi-C filtered, mergedEC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_FitHiC-filtered_merged_GM12878.bed
K562 MatchedFilterxESCAPExJEME integrative enhancer-target gene annotation, Hi-C filtered, mergedEC-003-CRE.MatchedFilterxESCAPExJEME-targetGene_FitHiC-filtered_merged_K562.bed
GM12878 MatchedFilterxESCAPExJEMExcRE compact integrative enhancer-target gene annotation, Hi-C filtered, mergedEC-003-CRE.hg19-cRExMatchedFilterxJEME_Hi-C_GM12878_merged.bed
K562 MatchedFilterxESCAPExJEMExcRE compact integrative enhancer-target gene annotation, Hi-C filtered, mergedEC-003-CRE.hg19-cRExMatchedFilterxJEME_Hi-C_K562_merged.bed
GM12878 MatchedFilterxESCAPExJEMExcRE compact integrative enhancer-target gene annotation, Hi-C filtered, merged, trimmed by TFBSEC-003-CRE.hg19-cRExMatchedFilterxJEME_Hi-C_GM12878_merged_trimmed.bed
K562 MatchedFilterxESCAPExJEMExcRE compact integrative enhancer-target gene annotation, Hi-C filtered, merged, trimmed by TFBSEC-003-CRE.hg19-cRExMatchedFilterxJEME_Hi-C_K562_merged_trimmed.bed

Extended genes

HepG2 P-value package for extended genesEC-003-EXT.pval_HepG2.tar.gz
K562 P-value package for extended genesEC-003-EXT.pval_K562.tar.gz
MCF-7 P-value package for extended genesEC-003-EXT.pval_MCF-7.tar.gz

Background mutation rate (BMR)

BMR detailed list of featuresEC-003-BMR.feature_details.txt
Covariate matrix 100kb resolutionEC-003-BMR.covariate_region_100kb.txt
Covariate matrix 1mb resolutionEC-003-BMR.covariate_region_1mb.txt
Description of BMR estimation parametersEC-003-BMR.README.txt
Blood cancer BMR estimation parameterEC-003-BMR.BloodCan_dispersion.txt
Blood cancer BMR estimation parameterEC-003-BMR.BloodCan_mu_nb.txt
Blood cancer BMR estimation parameterEC-003-BMR.BloodCan_mu_pois.txt
Blood cancer BMR estimation parameterEC-003-BMR.BloodCan_theta_nb.txt
Breast cancer BMR estimation parameterEC-003-BMR.BreastCan_dispersion.txt
Breast cancer BMR estimation parameterEC-003-BMR.BreastCan_mu_nb.txt
Breast cancer BMR estimation parameterEC-003-BMR.BreastCan_mu_pois.txt
Breast cancer BMR estimation parameterEC-003-BMR.BreastCan_theta_nb.txt
Liver cancer BMR estimation parameterEC-003-BMR.LiverCan_dispersion.txt
Liver cancer BMR estimation parameterEC-003-BMR.LiverCan_mu_nb.txt
Liver cancer BMR estimation parameterEC-003-BMR.LiverCan_mu_pois.txt
Liver cancer BMR estimation parameterEC-003-BMR.LiverCan_theta_nb.txt
Lung cancer BMR estimation parameterEC-003-BMR.LungCan_dispersion.txt
Lung cancer BMR estimation parameterEC-003-BMR.LungCan_mu_nb.txt
Lung cancer BMR estimation parameterEC-003-BMR.LungCan_mu_pois.txt
Lung cancer BMR estimation parameterEC-003-BMR.LungCan_theta_nb.txt

Regulatory score

TF regulatory score descriptionEC-003-DBP.regulatoryScore_README.txt
TF regulatory score packageEC-003-DBP.regulatoryScore.tar.gz
RBP regulatory score packageAvailable soon

Cell-type-specific network

TIP Profiles of ENCODE TF ChIP-seq experimentsEC-003-NET.ENCODE_TIP_Profiles_693.txt
GM12878 Proximal TIP-based networkEC-003-NET.edgeList_TIP_GM12878.tsv
K562 Proximal TIP-based networkEC-003-NET.edgeList_TIP_K562.tsv
GM12878 Proximal TSS-based network, using all TSS annotationsEC-003-NET.edgeList_TSS_GM12878.tsv
K562 Proximal TSS-based network, using all TSS annotationsEC-003-NET.edgeList_TSS_K562.tsv
GM12878 Distal enhancer-based networkEC-003-NET.edgeList_ENH_GM12878.tsv
K562 Distal enhancer-based networkEC-003-NET.edgeList_ENH_K562.tsv
A549 Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_A549.tsv
GM12878 Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_GM12878.tsv
H1-hESC Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_H1-hESC.tsv
HeLa-S3 Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_HeLa-S3.tsv
HepG2 Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_HepG2.tsv
IMR-90 Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_IMR-90.tsv
K562 Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_K562.tsv
MCF-10A Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_MCF-10A.tsv
MCF-7 Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_MCF-7.tsv
Liver Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_liver.tsv
Lung Proximal TSS-based network, using 1 TSS annotation per geneEC-003-NET.edgeList_uniqTSS2500_lung.tsv

Reconciled merged network

Proximal TIP-based merged networkEC-003-NET.mergedNet_TIP_FDR_0.1.tsv
Proximal TSS-based merged networkEC-003-NET.mergedNet_uniqTSS2500_ALL.tsv
Probability-based network descriptionEC-003-NET.probNet_README.txt
Probability-based TF networkEC-003-NET.probNet_TF.txt
Probability-based RBP networkEC-003-NET.probNet_RBP.txt
Gene ID conversion tableEC-003-NET.Ensemble2EntrezGeneID.tsv

Network hierachy

Merged network hierachy descriptionEC-003-NET.hierarchy_mergedNet_README.txt
Merged network hierachy, TIP-basedEC-003-NET.hierarchy_mergedNet_TFss.merged.TIP.network.txt
Merged network hierachy, mean t-valueEC-003-NET.hierarchy_mergedNet_tval.mean.across.patients.txt
Cell type specific network hierachy documentationEC-003-NET.hierarchy_cellTypeSpecNet_README.txt
Cell type specific network hierachy node propertiesEC-003-NET.hierarchy_cellTypeSpecNet_node.properties.txt
GM12878 network hierachyEC-003-NET.hierarchy_cellTypeSpecNet_GM12878.tfcom.ss.txt
K562 network hierachyEC-003-NET.hierarchy_cellTypeSpecNet_K562.tfcom.ss.txt

Network rewiring and rewiring index

CML proximal-distal combined TF-GENE network rewiring, TIP-basedEC-003-NET.KG_TIP_ENH_mnet.csv
CML proximal-distal combined TF-GENE network rewiring, TSS-basedEC-003-NET.KG_TSS_ENH_mnet.csv
CML proximal-distal combined TF-TF network rewiring, TIP-basedEC-003-NET.KG_TIP_ENH_tfnet.csv
CML proximal-distal combined TF-TF network rewiring, TSS-basedEC-003-NET.KG_TSS_ENH_tfnet.csv
TF attributes, TIP-basedEC-003-NET.KG_TIP_ENH_TFattrib.csv
TF attributes, TSS-basedEC-003-NET.KG_TSS_ENH_TFattrib.csv
GENE attributes, TIP-basedEC-003-NET.KG_TIP_ENH_GENEattrib.csv
GENE attributes, TSS-basedEC-003-NET.KG_TSS_ENH_GENEattrib.csv
CML rewiring index, direct connection, TIP-basedEC-003-NET.KG_rewiringIndex_TIP+ENH.csv
CML rewiring index, direct connection, TSS-basedEC-003-NET.KG_rewiringIndex_TSS+ENH.csv
CML rewiring index, gene community-basedEC-003-NET.KG_rewiringIndex-geneCommunity_TFrand_mixedM_median.txt
CML rewiring index, gene community-based, cubic-rootedEC-003-NET.KG_rewiringIndex-geneCommunity_TFrand_mixedM_median_cubicroot.txt

EN-CODEC.VALIDATION


Experimental validations

Luciferase CRE validation raw dataEC-004-CRE.luciferase_raw.csv
Luciferase CRE validation normalized dataEC-004-CRE.luciferase_normalized.csv
MYC knockdown experiment descriptionEC-004-DBP.README.txt
MYC siRNA controlEC-004-DBP.MYC-KD_geneFPKM_control.txt
MYC siRNA knockdownEC-004-DBP.MYC-KD_geneFPKM_knockdown.txt

EN-CODEC.SOFTWARE


Code releases

BMR software packageAvailable soon
ESCAPE software packageAvailable soon
Rewiring direct connection software packageEC-005-NET.Rewiring_directConnection_related.tar.gz
Rewiring mixed membership software packageEC-005-NET.Rewiring_geneCommunity_related.tar.gz

© Gerstein Lab, Yale University 2017