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Coexpression cluster:C884

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Full id: C884_Mesenchymal_Alveolar_Smooth_Renal_Pericytes_Fibroblast_Hepatic



Phase1 CAGE Peaks

  Short description
Hg19::chr11:62446527..62446572,- p1@UBXN1
Hg19::chr16:76269543..76269562,- p1@ENST00000478088
Hg19::chr19:49122427..49122447,- p1@RPL18
Hg19::chr19:49990853..49990871,+ p1@RPL13AP5
p1@RPL13A
Hg19::chr19:54704718..54704735,+ p1@RPS9
Hg19::chr19:55897297..55897303,+ p1@RPL28
Hg19::chr19:5690297..5690316,+ p1@RPL36
Hg19::chr8:144679575..144679593,- p1@EEF1D
Hg19::chr8:146017765..146017814,- p1@RPL8


Enriched pathways on this co-expression clusterSummary:
Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.
Analyst: Emmanuel Dimont

link to source dataset
data


p.valueFDRnGenesnPathwayName
6.50699372147126e-121.29778825489618e-09592Ribosome (KEGG):03010
6.8763067114908e-121.29778825489618e-09593Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
8.20087364863308e-121.29778825489618e-096296Metabolism of proteins (Reactome):REACT_17015
1.93996305375098e-112.45599322604874e-095114Regulation of beta-cell development (Reactome):REACT_13698
6.86687013595479e-116.20961256579912e-096421Gene Expression (Reactome):REACT_71
3.11609735119595e-092.4656120291338e-075312Diabetes pathways (Reactome):REACT_15380
6.12526308875603e-116.20961256579912e-095143Influenza Infection (Reactome):REACT_6167
0.0006597239851174110.04640058695325792162TNF alpha/NF-kB down reg. targets (Netpath):NetPath_9
7.97550775416383e-145.0484964083857e-116138{RPS27A,138} (Static Module):NA



Enriched Gene Ontology terms on this co-expression clusterSummary: Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0005830cytosolic ribosome (sensu Eukaryota)1.94711712698464e-11
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)7.33774794825837e-10
GO:0044445cytosolic part7.33774794825837e-10
GO:0033279ribosomal subunit1.26256280325865e-09
GO:0015934large ribosomal subunit1.82626324277862e-08
GO:0006412translation2.35185412760321e-08
GO:0005829cytosol7.70670491459429e-08
GO:0009059macromolecule biosynthetic process8.3730524348812e-08
GO:0044249cellular biosynthetic process2.59969019746735e-07
GO:0003735structural constituent of ribosome2.59969019746735e-07
GO:0005840ribosome3.65482119692358e-07
GO:0009058biosynthetic process8.35858825099753e-07
GO:0030529ribonucleoprotein complex1.33240308617928e-06
GO:0032991macromolecular complex1.12699311692551e-05
GO:0044444cytoplasmic part2.87888442874071e-05
GO:0003723RNA binding4.3211924777402e-05
GO:0019843rRNA binding6.73824644083435e-05
GO:0010467gene expression6.73824644083435e-05
GO:0044267cellular protein metabolic process7.35318134200805e-05
GO:0044260cellular macromolecule metabolic process7.54393068709226e-05
GO:0043232intracellular non-membrane-bound organelle8.09803016258299e-05
GO:0043228non-membrane-bound organelle8.09803016258299e-05
GO:0019538protein metabolic process8.09803016258299e-05
GO:0005737cytoplasm0.000337091277116998
GO:0044446intracellular organelle part0.000390228814677799
GO:0044422organelle part0.000390228814677799
GO:0003676nucleic acid binding0.00309843597899137
GO:0043170macromolecule metabolic process0.00315665668313737
GO:0044237cellular metabolic process0.00657747852642446
GO:0044238primary metabolic process0.00665292298190928
GO:0044424intracellular part0.00704833894383528
GO:0005853eukaryotic translation elongation factor 1 complex0.00938889893486113
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0128883939605573
GO:0005622intracellular0.0148927233606149
GO:0003746translation elongation factor activity0.0189162263226417
GO:0006414translational elongation0.02115428669203
GO:0043229intracellular organelle0.0263794238315517
GO:0043226organelle0.0263794238315517
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0314307297225802
GO:0043284biopolymer biosynthetic process0.0314307297225802
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.032772484148343
GO:0015935small ribosomal subunit0.0358088416844965
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0401259745596671
GO:0009967positive regulation of signal transduction0.0431192164746101
GO:0005730nucleolus0.0454276527307375



Enriched sample ontology terms on this co-expression clusterSummary:To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
epithelial vesicle3.00e-1078
somite3.48e-0871
presomitic mesoderm3.48e-0871
presumptive segmental plate3.48e-0871
dermomyotome3.48e-0871
trunk paraxial mesoderm3.48e-0871
vasculature8.62e-0878
vascular system8.62e-0878
multilaminar epithelium1.00e-0783
dense mesenchyme tissue1.22e-0773
paraxial mesoderm1.23e-0772
presumptive paraxial mesoderm1.23e-0772
vessel3.07e-0768
cardiovascular system3.54e-07109
skeletal muscle tissue8.16e-0762
striated muscle tissue8.16e-0762
myotome8.16e-0762


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary:The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.605294
MA0004.11.06719
MA0006.11.34805
MA0007.10.397529
MA0009.10.870971
MA0014.10.205864
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.12.15039
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.264106
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.22215
MA0056.10
MA0057.10.0725989
MA0058.11.56347
MA0059.10.323879
MA0060.10.9464
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.00178726
MA0074.10.509711
MA0076.10.901394
MA0077.10.832987
MA0078.10.607575
MA0081.11.55973
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.11.35827
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.11.366
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.406919
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.10.177438
MA0146.10.175555
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.21.95022
MA0035.21.19307
MA0039.20.109483
MA0138.20.608783
MA0002.20.152495
MA0137.20.780538
MA0104.20.486672
MA0047.20.542971
MA0112.20.378721
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.488402
MA0155.10.156896
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.11.14546
MA0160.10.453945
MA0161.10
MA0162.11.08366
MA0163.10.873334
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.0127399
MA0102.21.41188
MA0258.10.180288
MA0259.11.17199
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467512.47954140333821.89229392694668e-050.000429069225871439
BCL3#602311.51570093457940.001785915017827760.0109556052009934
BRCA1#67248.970769174766120.0006202690356731910.00514047594164993
CCNT2#90564.224134384641760.000840335063808250.00633764830510325
CEBPB#105154.428415347680450.00252258685237060.0139868575214872
E2F1#186963.271592809919550.003389959241809890.0172999732839181
E2F4#187457.037811286269130.0002942715148296660.00307242054756528
EGR1#195884.433936973164571.92853122912633e-050.00043530121685482
ELF1#199773.311853967961420.0008960205810173620.00666900609042704
ELK4#200559.019823143593359.04446507305493e-050.00132000403544548
ETS1#211355.40486717900130.00101160998680460.00717838941513018
FOSL2#2355611.28680040304113.04906898154755e-060.000103122317151504
GABPB1#255375.497087428141693.13640621886058e-050.000632727697685108
GATA1#262369.04020542920031.10995595465212e-050.000284472858767885
GTF2B#2959724.845201060039.99944740019878e-109.27470947628206e-08
GTF2F1#2962811.32414300156241.20451544008114e-088.97278088777707e-07
HEY1#2346283.591209816093969.88548321897326e-050.00139179021556531
IRF1#365986.788590003167916.86477102732501e-073.09697547007688e-05
JUND#372753.885924412150570.004544089270401160.0214800461352144
MAX#414975.018654284783325.77474544696214e-050.000962356214672537
MXI1#460155.534206460421830.000906612702046980.00660198884319373
MYC#460984.642028330319471.34916872863392e-050.000327231381444027
NFE2#4778217.15650236702870.005683079621106360.0256575088639056
NFKB1#479084.878278599283419.15949022225393e-060.000244531697168195
NFYA#480036.141860233276840.01048163163058090.0388160813370058
NR3C1#290846.65467703607690.001906862615018880.0112197647690117
NRF1#489968.140186298473942.03653511272495e-050.000451483104729105
PAX5#507975.187439857582764.62776729125731e-050.000812574626986588
POLR2A#543081.908847268051620.0116612289598830.0425760213718307
POU2F2#545277.082540933799745.66141070992737e-060.000170493677374309
RDBP#7936468.28373510667772.19241742291806e-071.16644871743321e-05
REST#597877.50557789032183.81690996642637e-060.000124768156489391
RFX5#599356.693283792886170.0003728115293534230.00370643153870939
SIN3A#2594263.605923151210090.002003057991334320.011646015340253
SIX5#147912713.28966749869037.60830171883304e-084.57457353605759e-06
SMARCB1#659848.112318124958850.0009076423789816390.00660764411114341
SP1#666774.43207440522070.0001322100940741540.00173793455192077
SP2#6668411.62379133059760.0002304904940995780.00253471588009538
STAT1#677249.202927776532980.0005628995032252660.00480299519749539
TAF1#687282.971596698440260.0004233749951234810.00395782859968683
TAF7#687978.892387314940821.20106539601475e-064.86194065482111e-05
TBP#690883.294907277419010.0001918853220272470.00231519306229248
TCF12#693855.908036056770230.0006689435531052020.00546451276830303
THAP1#55145413.94184204571170.0001142867648675440.00156414564749068
USF1#739174.947832771161756.35032938033638e-050.00103547548813888
USF2#739245.774309948919820.003223241005374920.0167005044084115
YY1#752884.365485110981212.17675027117712e-050.000479008895009413
ZNF143#770257.500486973459950.0002177465175801830.00249109744216855



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.