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Coexpression cluster:C896

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Full id: C896_retinoblastoma_iPS_acute_lymphoma_chronic_Burkitt_testicular



Phase1 CAGE Peaks

  Short description
Hg19::chr12:54674482..54674520,+ p1@HNRNPA1
Hg19::chr14:64855014..64855091,+ p1@MTHFD1
Hg19::chr18:19192235..19192337,+ p1@SNRPD1
Hg19::chr1:54303949..54303979,- p1@TMEM48
Hg19::chr2:9563769..9563832,+ p1@CPSF3
Hg19::chr4:57301896..57301945,+ p3@PAICS
Hg19::chr4:57302399..57302441,+ p1@PAICS
Hg19::chr6:8102752..8102806,- p1@EEF1E1
Hg19::chr8:4644826..4644848,+ p1@PAICSP4


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
3.49156482482783e-060.0007367201780386723134mRNA processing (Wikipathways):WP1863
1.57612000639245e-060.0004988419820232114421Gene Expression (Reactome):REACT_71
4.7073957674912e-060.0007449453802054833148mRNA Processing (Reactome):REACT_1675
7.12387426768043e-084.50941241144171e-054194{POLR2A,195} (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:0006397mRNA processing0.00271301856430786
GO:0016071mRNA metabolic process0.00271301856430786
GO:0044428nuclear part0.00271301856430786
GO:0000398nuclear mRNA splicing, via spliceosome0.00271301856430786
GO:0000375RNA splicing, via transesterification reactions0.00271301856430786
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.00271301856430786
GO:0051028mRNA transport0.00271301856430786
GO:0006396RNA processing0.00271301856430786
GO:0050658RNA transport0.00271301856430786
GO:0051236establishment of RNA localization0.00271301856430786
GO:0050657nucleic acid transport0.00271301856430786
GO:0006403RNA localization0.00271301856430786
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.00271301856430786
GO:0051292nuclear pore complex assembly0.00271301856430786
GO:0043517positive regulation of DNA damage response, signal transduction by p53 class mediator0.00271301856430786
GO:0043516regulation of DNA damage response, signal transduction by p53 class mediator0.00271301856430786
GO:0031081nuclear pore distribution0.00271301856430786
GO:0051664nuclear pore localization0.00271301856430786
GO:0046483heterocycle metabolic process0.00375888651171585
GO:0005681spliceosome0.00408093417500499
GO:0006999nuclear pore organization and biogenesis0.00465047824450652
GO:0006164purine nucleotide biosynthetic process0.00484923975527564
GO:0006163purine nucleotide metabolic process0.00505093545520049
GO:0006725aromatic compound metabolic process0.00505093545520049
GO:0004638phosphoribosylaminoimidazole carboxylase activity0.00505093545520049
GO:0004477methenyltetrahydrofolate cyclohydrolase activity0.00505093545520049
GO:0031503protein complex localization0.00505093545520049
GO:0004488methylenetetrahydrofolate dehydrogenase (NADP+) activity0.00505093545520049
GO:0009320phosphoribosylaminoimidazole carboxylase complex0.00505093545520049
GO:0003723RNA binding0.00601224402120285
GO:0004486methylenetetrahydrofolate dehydrogenase activity0.00610267470704545
GO:0004639phosphoribosylaminoimidazolesuccinocarboxamide synthase activity0.00610267470704545
GO:0008380RNA splicing0.00641648721647463
GO:0044237cellular metabolic process0.00641648721647463
GO:0046040IMP metabolic process0.00641648721647463
GO:0006189'de novo' IMP biosynthetic process0.00641648721647463
GO:0016155formyltetrahydrofolate dehydrogenase activity0.00641648721647463
GO:0006188IMP biosynthetic process0.00641648721647463
GO:0044238primary metabolic process0.00641648721647463
GO:0009165nucleotide biosynthetic process0.00681108494481145
GO:0000105histidine biosynthetic process0.00681108494481145
GO:0009076histidine family amino acid biosynthetic process0.00681108494481145
GO:0019238cyclohydrolase activity0.00681108494481145
GO:0009113purine base biosynthetic process0.00742737510308045
GO:0017056structural constituent of nuclear pore0.00742737510308045
GO:0048584positive regulation of response to stimulus0.00742737510308045
GO:0006379mRNA cleavage0.00808909795120509
GO:0043231intracellular membrane-bound organelle0.00808909795120509
GO:0043227membrane-bound organelle0.00808909795120509
GO:0006378mRNA polyadenylation0.00878397215086816
GO:0009117nucleotide metabolic process0.00920670492014003
GO:0004329formate-tetrahydrofolate ligase activity0.00920670492014003
GO:0006144purine base metabolic process0.00920670492014003
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0101610744609576
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0101610744609576
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0101946355089543
GO:0043631RNA polyadenylation0.0103962941467483
GO:0009086methionine biosynthetic process0.0103962941467483
GO:0009077histidine family amino acid catabolic process0.0103962941467483
GO:0006548histidine catabolic process0.0103962941467483
GO:0051668localization within membrane0.0103962941467483
GO:0005634nucleus0.0104898718485841
GO:0031124mRNA 3'-end processing0.0106702538866237
GO:0046112nucleobase biosynthetic process0.0106702538866237
GO:0030330DNA damage response, signal transduction by p53 class mediator0.0120048467004822
GO:0009067aspartate family amino acid biosynthetic process0.0125607805918415
GO:0030530heterogeneous nuclear ribonucleoprotein complex0.0129073440839092
GO:0006555methionine metabolic process0.0129073440839092
GO:0031123RNA 3'-end processing0.0133568403480145
GO:0006547histidine metabolic process0.0133568403480145
GO:0009075histidine family amino acid metabolic process0.0133568403480145
GO:0000097sulfur amino acid biosynthetic process0.0133568403480145
GO:0003727single-stranded RNA binding0.0133568403480145
GO:0032991macromolecular complex0.0143517521129979
GO:0005654nucleoplasm0.0146921544393844
GO:0009112nucleobase metabolic process0.0147501284471468
GO:0009167purine ribonucleoside monophosphate metabolic process0.0147509141632119
GO:0009168purine ribonucleoside monophosphate biosynthetic process0.0147509141632119
GO:0030532small nuclear ribonucleoprotein complex0.0147509141632119
GO:0009127purine nucleoside monophosphate biosynthetic process0.0147509141632119
GO:0009126purine nucleoside monophosphate metabolic process0.0147509141632119
GO:0043229intracellular organelle0.0147509141632119
GO:0043226organelle0.0147509141632119
GO:0044249cellular biosynthetic process0.0153285431293036
GO:0005941unlocalized protein complex0.0153285431293036
GO:0044446intracellular organelle part0.0153285431293036
GO:0044422organelle part0.0153285431293036
GO:0009066aspartate family amino acid metabolic process0.0155011953877277
GO:0000096sulfur amino acid metabolic process0.0158730168833439
GO:0006405RNA export from nucleus0.0160580573782975
GO:0000245spliceosome assembly0.0160580573782975
GO:0009161ribonucleoside monophosphate metabolic process0.0172794177673077
GO:0009156ribonucleoside monophosphate biosynthetic process0.0172794177673077
GO:0016646oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor0.0176120875006243
GO:0016874ligase activity0.0177508126499261
GO:0048583regulation of response to stimulus0.0177508126499261
GO:0046148pigment biosynthetic process0.018313385097542
GO:0006997nuclear organization and biogenesis0.018313385097542
GO:0009124nucleoside monophosphate biosynthetic process0.018313385097542
GO:0009123nucleoside monophosphate metabolic process0.018313385097542
GO:0009396folic acid and derivative biosynthetic process0.018313385097542
GO:0031981nuclear lumen0.0187839884277303
GO:0042440pigment metabolic process0.0198410709876166
GO:0042770DNA damage response, signal transduction0.0201163796120492
GO:0051168nuclear export0.0201940384489898
GO:0006760folic acid and derivative metabolic process0.0201940384489898
GO:0044272sulfur compound biosynthetic process0.0204581691664226
GO:0065003macromolecular complex assembly0.0211608155288724
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0218602066024701
GO:0009058biosynthetic process0.0227569158174758
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.0227745621898682
GO:0019748secondary metabolic process0.0230032491780804
GO:0022607cellular component assembly0.0232599132872617
GO:0016831carboxy-lyase activity0.0238725883458216
GO:0003697single-stranded DNA binding0.0257665731809479
GO:0046907intracellular transport0.0281202584035222
GO:0043623cellular protein complex assembly0.0283847522894954
GO:0065002intracellular protein transport across a membrane0.0283847522894954
GO:0044424intracellular part0.0288803720298249
GO:0010467gene expression0.0302607832292535
GO:0031974membrane-enclosed lumen0.0302607832292535
GO:0043233organelle lumen0.0302607832292535
GO:0005515protein binding0.0319526487732182
GO:0016830carbon-carbon lyase activity0.0319526487732182
GO:0033036macromolecule localization0.0319526487732182
GO:0008652amino acid biosynthetic process0.0323185505394083
GO:0006790sulfur metabolic process0.0325652914814427
GO:0005643nuclear pore0.0325652914814427
GO:0009063amino acid catabolic process0.0326856938226464
GO:0009310amine catabolic process0.0350222804975169
GO:0044270nitrogen compound catabolic process0.0353154754539087
GO:0051649establishment of cellular localization0.0353154754539087
GO:0046930pore complex0.0353154754539087
GO:0051170nuclear import0.0354101628056411
GO:0051641cellular localization0.0362188448013473
GO:0030529ribonucleoprotein complex0.0366795809431643
GO:0044453nuclear membrane part0.0391841976045881
GO:0016043cellular component organization and biogenesis0.040027704534505
GO:0009309amine biosynthetic process0.041374638916086
GO:0006752group transfer coenzyme metabolic process0.0475581868919423
GO:0022618protein-RNA complex assembly0.0475588805752745
GO:0044271nitrogen compound biosynthetic process0.0495576642363756
GO:0009152purine ribonucleotide biosynthetic process0.0495576642363756



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

disease_data


Cell Type
Ontology termp-valuen
animal cell3.05e-21679
eukaryotic cell3.05e-21679
epithelial cell1.07e-15253
native cell9.21e-15722
embryonic cell3.53e-08250
Disease
Ontology termp-valuen
disease of cellular proliferation2.60e-54239
cancer2.82e-54235
organ system cancer8.23e-27137
cell type cancer3.65e-26143
carcinoma2.49e-22106
hematologic cancer4.15e-2151
immune system cancer4.15e-2151
leukemia4.55e-1739
myeloid leukemia3.40e-1331


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)
MA0003.10.818094
MA0004.11.06719
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.367355
MA0017.10.301634
MA0019.10.558663
MA0024.13.019
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
MA0055.10.0199484
MA0056.10
MA0057.11.37904
MA0058.10.86817
MA0059.11.55919
MA0060.12.16206
MA0061.10.432181
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.11.61616
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.931587
MA0091.10.417885
MA0092.10.381858
MA0093.11.35827
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.746654
MA0103.10.257174
MA0105.10.229733
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.959847
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.10.83188
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.11.51455
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.11.90392
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.10.177438
MA0146.10.51271
MA0147.11.7891
MA0148.10.439278
MA0149.10.464973
MA0062.21.95022
MA0035.20.473658
MA0039.20.679176
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.21.50683
MA0047.20.542971
MA0112.20.674448
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
MA0159.10.60858
MA0160.10.453945
MA0161.10
MA0162.10.294626
MA0163.10.101664
MA0164.10.583138
MA0080.20.268439
MA0018.21.36887
MA0099.20.481058
MA0079.20.48507
MA0102.21.41188
MA0258.10.532421
MA0259.11.82941
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
BCLAF1#977449.623398937831930.0004748877913943970.00433273399540835
BRCA1#67248.970769174766120.0006202690356731910.00514088388355467
CCNT2#90553.520111987201460.007045560226413870.0293944499055822
CHD2#110666.896015222744575.28898897155739e-050.000897735607346794
E2F1#186984.36212374655942.18983367577486e-050.000480975897506311
E2F4#187468.445373543522961.64629101974599e-050.000380055233888707
E2F6#187673.902232235764630.0003067423599492730.00316247436631216
ELF1#199773.311853967961420.0008960205810173620.0066694813955436
EP300#203353.763300959012890.005242178461590750.024286380532763
ETS1#211366.485840614801567.51193928811803e-050.00116331469055718
GABPB1#255353.926491020101210.004337976092287310.0205858726418754
HEY1#2346283.591209816093969.88548321897326e-050.00139216556351989
HMGN3#932454.543637624083660.002244618319024410.0128911571416327
IRF1#365965.091442502375930.0002963609703320.00309392676734344
IRF3#3661315.66065073716320.0007351478720625020.00579326255265492
MAX#414964.301703672671410.0007597563851723660.00596827356983954
MXI1#460177.747889044590563.07469224127045e-060.000103686723598981
MYC#460974.061774789029540.0002355556796573370.00256797490894913
NFKB1#479063.658708949462560.001850649648602720.0109339819341755
NFYA#480036.141860233276840.01048163163058090.038817457744982
NFYB#480135.586597751178820.01358500277111940.0479503904969054
NRF1#489968.140186298473942.03653511272495e-050.000451674858012065
PAX5#507953.705314183987680.005616557077719420.0253901053819823
POLR2A#543081.908847268051620.0116612289598830.0425804870757715
REST#597844.288901651612450.009457025945962830.0356641269867268
RFX5#599345.354627034308930.004249445027674740.0202208761274523
SIN3A#2594274.206910343078440.0001867843656174470.00226017522427535
SP1#666785.06522789168086.82787133058497e-060.000198412925402049
SP2#666838.71784349794820.003945531750578630.0189438851829111
TAF1#687282.971596698440260.0004233749951234810.00395924616007354
TAF7#687967.622046269949282.97588074999805e-050.000616418107197633
TBP#690883.294907277419010.0001918853220272470.00231546056004664
TRIM28#1015536.196841681754170.0102278065029780.0380827082378878
USF1#739164.240999518138640.0008220017441944160.00626041275883618
YY1#752873.819799472108550.0003529672812141940.00353641115528868
ZBTB33#10009414.07321112443610.000110211680217430.00153186021695877



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.


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