Cell type-selective disease-association of genes under high regulatory load

Cell type-selective disease-association of genes under high

regulatory load

Mafalda Galhardo, Philipp Berninger, Thanh-Phuong Nguyen, Thomas Sauter and Lasse Sinkkonen

Galhardo et al.: Cell type-selective disease-association of genes under high regulatory load

Supplementary Figures

Supplementary Figure S1: TF load enriches similar bins of enhancer load. Heatmaps of the

hypergeometric distribution enrichment significance (adjusted -log10p-value) of genes binned by TF load (y-axis) across different bins based on enhancer load (x-axis) for 9 ENCODE cell lines (from top to bottom, left to right: HUVEC, HCT116, MCF7, A549, HeLaS3, H1hESC, HepG2, K562 and GM12878). Genes were sorted by regulatory load and grouped in bins (y- and x-axis). Bottom or left side bins contain genes with lower regulatory load than top or right side bins. Bins denoted with “1” contain genes with no associated TF or enhancer. The enrichment significance (adjusted -log10p-value) is depicted by the color gradient, increasing from yellow to red (values ≥ 50 appear in red). Dark grey represents (adjusted -log10p-value) < 1.3, not considered significant. The significance is evident along the diagonal for all 9 cell lines, denoting the concerted increase between TF and enhancer load, with genes in bins of low TF load enriching the highest for genes in bins of low enhancer load and vice-versa, genes of high TF load enriching the most for high enhancer load genes. Supplementary File 5 contains tables with the enrichment significance (adjusted -log10p-value) obtained and the exact TF load per bin (vertically) or enhancer load per bin (horizontally) for each of 9 cell lines.

Supplementary Figure S2: High enhancer load genes enrich for disease association also with more stringent disease gene groups. Heatmaps of the hypergeometric distribution

enrichment significance (adjusted -log10p-value) is depicted by the color gradient, increasing from yellow to red. Grey represents (adjusted -log10p-value) < 1.3 (equivalent to p-value > 0.05), not considered significant. The significance is evident on the bins of highest enhancer load on the right side, with orange and red colours. (A) Results using the set of curated disease genes from DisGeNET version 2, minimum association score of 0.2 (7110 genes of which 5853 were in the background set of 19238 protein coding genes). (B) Results using the set of disease genes from the OMIM database, as of June 2015 (4557 genes of which 3483 were in the background set of 19238 protein coding genes).

Supplementary Figure S3: Genes with highest enhancer load vary across 139 samples.

Heatmap of the Jaccard similarity index for the pair-wise comparison of genes in the top enhancer load bin across 139 samples. The heatmap is mirrored along the diagonal. Blue denotes few common while red denotes many common genes on the two sets of highest enhancer load genes from any two samples. The predominance of the blue colour reflects an overall low similarity between the genes with highest enhancer load across samples (average similarity lower than 30%). The bottom and right-side color bars denote groups of samples with the same tissue of origin, color-coded on the bottom.

Supplementary Figure S4: Cell type-selective disease-association of genes under high regulatory load. Heatmap from Figure 4 showing the statistical significance (adjusted -log10

Galhardo et al.: Cell type-selective disease-association of genes under high regulatory load

and 174 diseases with names of the diseases and samples written out for each case. For more details, see Supplementary File 4.

Supplementary Figure S5: Liver disease gene network. Illustration of the reconstructed liver

disease gene network containing 3,775 genes and 8,278 interactions. Red nodes represent the high regulatory load genes from the two liver samples (primary liver (E066) and HepG2) and grey nodes the other liver disease genes and their first neighbours in the network. A higher intensity of red color is observed on the central area of the network, reflecting the higher betweenness centrality of the high regulatory load genes as described in Figure 6.

Supplementary Figure S6: HRL genes have longer CDS and transcripts on average. (A)

Supplementary Figure S1

0 10 20 30 40 50

(-log₁₀p-value)

Enrichment significance of TF & enhancer load correlation

TF load (binned) 1 2 3 4 5 1 2 3 4 5 6 7 8 9 10 11 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 1 2 3 4 5 1 2 3 4 5 6 7 8 9 10 11 A549 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 9 10 11 H1hESC 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 9 10 11 HepG2 1 2 3 4 5 6 7 1 2 3 4 5 6 7 8 9 10 11 HeLaS3 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 9 10 11 K562 1 2 3 4 5 6 7 8 9 1 2 3 4 5 6 7 8 9 10 11 GM12878 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 9 10 11

A B A549−EtOHAG04450 CellLine.GerminalCenterBCellLike.BP_KARPAS−422_c01CellLine.GerminalCenterBCellLike.BP_SU−DHL−5_c01 CellLine.MantleCellLymphoma.BP_JVM−2_c01CellLine.MantleCellLymphoma.BP_Z−138_c01 CellLine.MultipleMyeloma.BP_U−266_c01 CellLine.SporadicBurkittLymphoma.BP_BL−2_c01 CellLine.SporadicBurkittLymphoma.BP_DG−75_c01CordBlood.AltActMacrophage.S00C1HH1 CordBlood.CD8+_naive.C002YMH1CordBlood.Erythroblast.S002R5H1 CordBlood.Erythroblast.S002S3H1 CordBlood.Megakaryocyte.S004BTH2CordBlood.Monocyte.C00264H1 CordBlood.Monocyte.C005PSH2 CordBlood.Monocyte.S000RDH2 CordBlood.Neutrophil.C00184H2 CordBlood.Neutrophil.C004GDH1Dnd41 E003 E004 E005 E006 E007 E008 E011 E012 E013 E014 E015 E016 E017 E019 E020 E021 E022 E026 E029 E032 E034 E037 E038 E039 E040 E041 E042 E043 E044 E045 E046 E047 E048 E049 E050 E055 E056 E058 E059 E061 E062 E063 E065 E066 E067 E068 E069 E071 E072 E073 E074 E075 E076 E078 E079 E080 E084 E085 E087 E089 E090 E091 E092 E093 E094 E095 E096 E097 E098 E099 E100 E101 E102 E103 E104 E105 E106 E108 E109 E111 E112 E113 GM12878H1hESC HCT116HMEC HSMM HUVEC HeLaS3HepG2 K562 MCF7 Monocd14ro1746NHA NHDFAdNHEK NHLF Osteo PANC1 VenousBlood.AltActMacrophage.S00622H1VenousBlood.AltActMacrophage.S006VIH1 VenousBlood.AltActMacrophage.S00BS4H1VenousBlood.CD4+_TCell.C002Q1H1 VenousBlood.CD4+_TCell.C002TWH1VenousBlood.CD4+_TCell.S007DDH2 VenousBlood.InflammatoryMacrophage.S001MJH1VenousBlood.InflammatoryMacrophage.S001S7H2 VenousBlood.InflammatoryMacrophage.S0022IH2VenousBlood.MatureEosinophil.S00BKKH1 VenousBlood.Monocyte.C000S5H2 VenousBlood.Monocyte.C0010KH1VenousBlood.Monocyte.C0011IH1 VenousBlood.Monocyte.C001UYH2 VenousBlood.Monocyte.C004SQH1 VenousBlood.Neutrophil.C000S5H1 VenousBlood.Neutrophil.C0010KH2VenousBlood.Neutrophil.C0011IH2 VenousBlood.Neutrophil.C001UYH1VenousBlood.Neutrophil.C12012H1 Supplementary Figure S2 (-log₁₀p-value)0 5 10 15 20 25 30 35 Disease association enrichment significance A549−EtOHAG04450 CellLine.GerminalCenterBCellLike.BP_KARPAS−422_c01CellLine.GerminalCenterBCellLike.BP_SU−DHL−5_c01 CellLine.MantleCellLymphoma.BP_JVM−2_c01CellLine.MantleCellLymphoma.BP_Z−138_c01 CellLine.MultipleMyeloma.BP_U−266_c01 CellLine.SporadicBurkittLymphoma.BP_BL−2_c01 CellLine.SporadicBurkittLymphoma.BP_DG−75_c01CordBlood.AltActMacrophage.S00C1HH1 CordBlood.CD8+_naive.C002YMH1CordBlood.Erythroblast.S002R5H1 CordBlood.Erythroblast.S002S3H1 CordBlood.Megakaryocyte.S004BTH2CordBlood.Monocyte.C00264H1 CordBlood.Monocyte.C005PSH2 CordBlood.Monocyte.S000RDH2 CordBlood.Neutrophil.C00184H2 CordBlood.Neutrophil.C004GDH1Dnd41 E003 E004 E005 E006 E007 E008 E011 E012 E013 E014 E015 E016 E017 E019 E020 E021 E022 E026 E029 E032 E034 E037 E038 E039 E040 E041 E042 E043 E044 E045 E046 E047 E048 E049 E050 E055 E056 E058 E059 E061 E062 E063 E065 E066 E067 E068 E069 E071 E072 E073 E074 E075 E076 E078 E079 E080 E084 E085 E087 E089 E090 E091 E092 E093 E094 E095 E096 E097 E098 E099 E100 E101 E102 E103 E104 E105 E106 E108 E109 E111 E112 E113 GM12878H1hESC HCT116HMEC HSMM HUVEC HeLaS3HepG2 K562 MCF7 Monocd14ro1746NHA NHDFAdNHEK NHLF Osteo PANC1 VenousBlood.AltActMacrophage.S00622H1VenousBlood.AltActMacrophage.S006VIH1 VenousBlood.AltActMacrophage.S00BS4H1VenousBlood.CD4+_TCell.C002Q1H1 VenousBlood.CD4+_TCell.C002TWH1VenousBlood.CD4+_TCell.S007DDH2 VenousBlood.InflammatoryMacrophage.S001MJH1VenousBlood.InflammatoryMacrophage.S001S7H2 VenousBlood.InflammatoryMacrophage.S0022IH2VenousBlood.MatureEosinophil.S00BKKH1 VenousBlood.Monocyte.C000S5H2 VenousBlood.Monocyte.C0010KH1VenousBlood.Monocyte.C0011IH1 VenousBlood.Monocyte.C001UYH2 VenousBlood.Monocyte.C004SQH1 VenousBlood.Neutrophil.C000S5H1 VenousBlood.Neutrophil.C0010KH2VenousBlood.Neutrophil.C0011IH2 VenousBlood.Neutrophil.C001UYH1VenousBlood.Neutrophil.C12012H1 (-log₁₀p-value) Disease association enrichment significance 0 2 4 6 8

Curated disease genes

Supplementary Figure S3 BL O SP LE TH Y M HEART COLON _BREAST

STOMACH _PANCREAS MUSCLE _PLACENTA

SMALL INTESTINE RECTUM ESOPHAGUS LUNG _LIVER FETAL INTESTINE SKIN OVARY VASCULAR

DUODENUM (MUSCLE) STOMACH (MUSCLE)

COLON (MUSCLE)

RECTUM (MUSCLE) ADRENAL GLAND

BONE _BRAIN

CERVIX

PLACENTA MUSCLE STOMACH MUSCLE

LIVER LUNG SKIN

BREAST SKIN VASCULAR SKIN _LUNG MUSCLE LUNG LUNG PANCREAS BRAIN PANCREAS SKIN 0.2 0.4 0.6 0.8 1 0

Supplementary Figure S4

Myocardial Reperfusion InjuryBrain Ischemia Arthritis, Experimental Lupus Erythematosus, SystemicSepsis Dermatitis, Allergic ContactMultiple Sclerosis Celiac DiseaseSeizures Brain InjuriesMelanoma Cocaine−Related DisordersHyperalgesia Alzheimer Disease Carcinoma, Squamous CellGlioma Urinary Bladder NeoplasmsPain Amphetamine−Related DisordersCardiomyopathies Kidney Failure, ChronicInsulin Resistance Epilepsy Cholestasis Endotoxemia Esophageal Squamous Cell CarcinomaAtherosclerosis Glomerulonephritis Intellectual DisabilityColitis HypothyroidismFibrosis Dermatitis, Atopic Nephrotic SyndromeBurns Cardiomyopathy, DilatedMetabolic Syndrome X Small Cell Lung CarcinomaBipolar Disorder Calcinosis Leukemia, Lymphocytic, Chronic, B−CellNeuroblastoma Fetal Growth RetardationKeloid Leukemia Hyperlipidemias Enterocolitis, NecrotizingHyperplasia Non−alcoholic Fatty Liver DiseaseAcute Coronary Syndrome Diabetes MellitusHyperinsulinism Kidney NeoplasmsAlbuminuria Neural Tube DefectsAdenoma Anti−Glomerular Basement Membrane DiseaseCarcinoma, Transitional Cell Stomach Ulcer Cardiomyopathy, HypertrophicDiabetic Neuropathies Pancreatitis, Acute NecrotizingMuscular Atrophy Uremia Ureteral ObstructionBrain Neoplasms Deafness Hypertension, EssentialAmnesia Brain Edema Dyskinesia, Drug−InducedBrain Infarction Gliosis Hypertrophy, Right VentricularRenal Insufficiency Carcinoma, Pancreatic Ductal Glomerulonephritis, MembranoproliferativeLung Injury Migraine DisordersFemoral Fractures Limb Deformities, CongenitalMalaria Acute−Phase Reaction Polycystic Kidney Diseases Diabetes Mellitus, ExperimentalDiabetes Mellitus, Type 2 Myocardial Ischemia Mammary Neoplasms, ExperimentalCarcinoma Endometriosis Mammary Neoplasms, AnimalArthritis, Rheumatoid Leukemia, Myeloid, AcuteProstatic Neoplasms Breast NeoplasmsLung Neoplasms Craniofacial AbnormalitiesColonic Neoplasms Liver Neoplasms Carcinoma, Adenoid CysticWeight Gain Hypertension, Pulmonary Cell Transformation, NeoplasticGlioblastoma Heart Defects, CongenitalObesity InflammationAsthma Drug−Induced Liver InjuryKidney Diseases Esophageal Neoplasms Encephalomyelitis, Autoimmune, ExperimentalLiver Diseases Osteoporosis Colitis, UlcerativeSkin Diseases Psoriasis Arsenic PoisoningHypersensitivity Pneumonia PancreatitisProteinuria Skin NeoplasmsCrohn Disease Neurotoxicity SyndromesHypertension, Portal Erectile Dysfunction Leukemia, Promyelocytic, AcuteAutistic Disorder Schizophrenia Substance−Related Disorders Child Development Disorders, PervasiveHemangiosarcoma Diabetes Mellitus, Type 1 Amyotrophic lateral sclerosis 1Medulloblastoma Precursor Cell Lymphoblastic Leukemia−LymphomaChloracne Burkitt Lymphoma Peripheral Nervous System DiseasesStomach Neoplasms Colorectal Neoplasms Liver Cirrhosis, Experimental Liver Neoplasms, ExperimentalAbortion, Spontaneous Adenocarcinoma Carcinoma, Non−Small−Cell LungOvarian Neoplasms Diabetic NephropathiesStroke Nerve Degeneration Pancreatic NeoplasmsPulmonary Fibrosis Coronary Artery Disease Hypertrophy, Left VentricularLiver Cirrhosis Salivary Gland NeoplasmsHernia, Diaphragmatic Endometrial NeoplasmsCleft Palate Glomerulosclerosis, Focal SegmentalAtrial Fibrillation Congenital diaphragmatic herniaEye Abnormalities Hypertension Reperfusion Injury Carcinoma, HepatocellularMyocardial Infarction Neoplasm MetastasisHeart Failure Cardiomegaly Spinal Cord Injuries Neoplasm InvasivenessLung Diseases

E003 E004 E007 E008 E011 E012 E014 E016 E019 E020 E067 E068 E069 E071 E072 E073 E074

H1hESC CellLin e.Ge rminalCenterBCellLi ke .BP_KAR PAS.422_c01 CellLin e.Ge rminalCenterBCellLi ke .BP_SU.DHL.5_c01 CellLin e.MantleCell Lymphoma.BP_JVM.2_c01 CellLin e.MantleCell Lymphoma.BP_Z.138_c01 CellLin e.MultipleM yeloma.BP_U.266_c01 CellLin e.Spo radicBu rkitt Lymphoma.BP_BL.2_c01 CellLin e.Spo radicBu rkitt Lymphoma.BP_DG.75_c01 CordBlood.AltActMacrophag e.S00C1HH1 CordBlood.E rythro blast.S002R5H1 CordBlood.E rythro blast.S002S3H1 CordBlood.Megaka ry ocyt e.S004BTH2

Dnd41 E032 E050 E059 E061 E087

GM12878 K562 MCF7 VenousBlood.CD4._TCell.C002TWH1CordBlood.CD8._nai ve .C002YMH1 CordBlood.Monocyt e.S000RDH2

E037 E039 E041 E044 E045 E047 E062

VenousBlood.AltActMacrophag e.S006VIH1 VenousBlood.AltActMacrophag e.S00BS4H1 VenousBlood.CD4._TCell.C002Q1H1 VenousBlood.Inflammato ryMacrophag e.S0022IH2 VenousBlood.MatureEosinophil.S00BKKH1 CordBlood.Monocyt e.C00264H1 CordBlood.Monocyt e.C005PSH2 CordBlood.Neutrophil.C00184H2 CordBlood.Neutrophil.C004GDH1 E029 VenousBlood.AltActMacrophag e.S00622H1 VenousBlood.Inflammato ryMacrophag e.S001MJH1 VenousBlood.Inflammato ryMacrophag e.S001S7H2 VenousBlood.Monocyt e.C000S5H2 VenousBlood.Monocyt e.C0010KH1 VenousBlood.Monocyt e.C0011IH1 VenousBlood.Monocyt e.C001UYH2 VenousBlood.Monocyt e.C004SQH1

VenousBlood.Neutrophil.C000S5H1 VenousBlood.Neutrophil.C0010KH2 VenousBlood.Neutrophil.C0011IH2VenousBlood.Neutrophil.C001UYH1 VenousBlood.Neutrophil.C12012H1 E034 E038 E040 E042 E043 E046 E048 E109 E112

VenousBlood.CD4._TCell.S007DDH2

A549.EtOHAG04450

E005 E006 E015 E017 E026 E049 E055 E056 E063 E065 E066 E075 E078 E079 E080 E084 E085 E089 E090 E091 E092 E093 E094 E095 E096 E097 E099 E101 E102 E103 E104 E105 E106 E113 HCT116HMEC HSMM HUVEC HeLaS3NHANHD

FAd

NHEK NHLF Osteo PANC1 E013 E021 E022 E058 E076 E098 E100 E108 E111 HepG2

Supplementary Figure S6 A B C 50 100 200 500 1000 2000 5000 20000 50000 0.0 0.2 0.4 0.6 0.8 1.0 cds length cum ulativ e fr action

5e+02 5e+03 5e+04 5e+05

0.0 0.2 0.4 0.6 0.8 1.0

unspliced transcript length

cum ulativ e fr action 0 5000 10000 15000 20000 25000 0 10000 20000 30000 40000 3' UTR length CDS length Cumulative fraction of CDSs

Cumulative fraction of transcripts

CDS length (nt) Unspliced transcript length (nt)