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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 10:51, 17 September 2013


Full id: C185_small_adrenal_gastric_Mesenchymal_acute_HES3GFP_testis



Phase1 CAGE Peaks

Hg19::chr10:121863383..121863387,-p@chr10:121863383..121863387
-
Hg19::chr10:121863435..121863446,-p@chr10:121863435..121863446
-
Hg19::chr10:133457602..133457623,+p@chr10:133457602..133457623
+
Hg19::chr10:36850273..36850276,-p@chr10:36850273..36850276
-
Hg19::chr10:66459172..66459188,-p@chr10:66459172..66459188
-
Hg19::chr10:67571401..67571408,-p@chr10:67571401..67571408
-
Hg19::chr11:102647098..102647117,-p@chr11:102647098..102647117
-
Hg19::chr11:31093041..31093047,-p@chr11:31093041..31093047
-
Hg19::chr11:31171048..31171052,+p@chr11:31171048..31171052
+
Hg19::chr11:31391345..31391358,+p3@DNAJC24
Hg19::chr11:31832461..31832468,-p20@PAX6
Hg19::chr11:67351250..67351261,+p2@GSTP1
Hg19::chr11:68519026..68519037,-p5@MTL5
Hg19::chr11:76973897..76973898,-p@chr11:76973897..76973898
-
Hg19::chr12:88178319..88178329,-p2@MKRN9P
Hg19::chr13:104517168..104517170,+p@chr13:104517168..104517170
+
Hg19::chr13:92569013..92569022,-p@chr13:92569013..92569022
-
Hg19::chr13:92571088..92571098,-p@chr13:92571088..92571098
-
Hg19::chr13:92571252..92571265,-p@chr13:92571252..92571265
-
Hg19::chr15:36739964..36739979,-p@chr15:36739964..36739979
-
Hg19::chr15:96903700..96903704,+p@chr15:96903700..96903704
+
Hg19::chr15:96959907..96959930,+p@chr15:96959907..96959930
+
Hg19::chr15:97503439..97503472,+p@chr15:97503439..97503472
+
Hg19::chr15:97554594..97554599,-p@chr15:97554594..97554599
-
Hg19::chr15:97777487..97777525,+p@chr15:97777487..97777525
+
Hg19::chr15:97779038..97779056,+p@chr15:97779038..97779056
+
Hg19::chr16:84424157..84424178,-p@chr16:84424157..84424178
-
Hg19::chr17:58979826..58979836,+p@chr17:58979826..58979836
+
Hg19::chr1:47881953..47881958,+p1@FOXE3
Hg19::chr1:63789403..63789435,-p1@ENST00000431294
Hg19::chr1:81686906..81686911,+p@chr1:81686906..81686911
+
Hg19::chr1:81771995..81772012,+p4@LPHN2
Hg19::chr1:81772013..81772038,+p10@LPHN2
Hg19::chr1:81772072..81772104,+p3@LPHN2
Hg19::chr1:81772113..81772122,+p17@LPHN2
Hg19::chr20:50722573..50722580,-p18@ZFP64
Hg19::chr20:52871134..52871139,-p@chr20:52871134..52871139
-
Hg19::chr21:16662950..16662957,-p@chr21:16662950..16662957
-
Hg19::chr21:26144899..26144920,-p@chr21:26144899..26144920
-
Hg19::chr21:26151976..26151979,+p@chr21:26151976..26151979
+
Hg19::chr2:189756256..189756260,+p@chr2:189756256..189756260
+
Hg19::chr2:200324103..200324118,-p@chr2:200324103..200324118
-
Hg19::chr3:102157364..102157394,+p@chr3:102157364..102157394
+
Hg19::chr3:177715091..177715094,+p@chr3:177715091..177715094
+
Hg19::chr3:78334430..78334433,-p@chr3:78334430..78334433
-
Hg19::chr3:78360347..78360353,+p@chr3:78360347..78360353
+
Hg19::chr3:78360522..78360543,+p@chr3:78360522..78360543
+
Hg19::chr3:78666867..78666875,-p43@ROBO1
Hg19::chr3:78684981..78684990,-p@chr3:78684981..78684990
-
Hg19::chr3:78685050..78685061,-p@chr3:78685050..78685061
-
Hg19::chr3:86289712..86289720,+p@chr3:86289712..86289720
+
Hg19::chr3:86701885..86701893,-p@chr3:86701885..86701893
-
Hg19::chr3:86701902..86701920,-p@chr3:86701902..86701920
-
Hg19::chr3:86701921..86701925,-p@chr3:86701921..86701925
-
Hg19::chr3:86703134..86703137,-p@chr3:86703134..86703137
-
Hg19::chr3:86703154..86703166,-p@chr3:86703154..86703166
-
Hg19::chr3:86703174..86703181,-p@chr3:86703174..86703181
-
Hg19::chr4:145430439..145430458,-p@chr4:145430439..145430458
-
Hg19::chr4:157516018..157516023,+p@chr4:157516018..157516023
+
Hg19::chr4:160188990..160189002,+p16@RAPGEF2
Hg19::chr4:160189041..160189050,+p37@RAPGEF2
Hg19::chr4:160189282..160189289,+p38@RAPGEF2
Hg19::chr4:183370111..183370118,+p12@ODZ3
Hg19::chr4:20482109..20482123,+p@chr4:20482109..20482123
+
Hg19::chr5:103559627..103559633,-p@chr5:103559627..103559633
-
Hg19::chr5:103559757..103559775,+p@chr5:103559757..103559775
+
Hg19::chr5:124228937..124228942,+p@chr5:124228937..124228942
+
Hg19::chr5:50262633..50262637,+p@chr5:50262633..50262637
+
Hg19::chr5:80703757..80703760,-p1@AK054959
Hg19::chr5:91378410..91378419,+p1@ENST00000507217
Hg19::chr6:10074344..10074351,-p@chr6:10074344..10074351
-
Hg19::chr6:121655552..121655592,-p4@C6orf170
Hg19::chr6:122403849..122403854,-p@chr6:122403849..122403854
-
Hg19::chr6:122720681..122720713,+p3@HSF2
Hg19::chr6:129513919..129513922,+p@chr6:129513919..129513922
+
Hg19::chr6:140771120..140771128,+p@chr6:140771120..140771128
+
Hg19::chr6:141460346..141460355,+p@chr6:141460346..141460355
+
Hg19::chr6:141715304..141715307,+p@chr6:141715304..141715307
+
Hg19::chr6:64762702..64762707,+p@chr6:64762702..64762707
+
Hg19::chr7:84390545..84390550,+p@chr7:84390545..84390550
+
Hg19::chr7:84651769..84651772,-p@chr7:84651769..84651772
-
Hg19::chr7:84651785..84651813,-p@chr7:84651785..84651813
-
Hg19::chr7:84651827..84651832,-p@chr7:84651827..84651832
-
Hg19::chr7:85204085..85204091,+p@chr7:85204085..85204091
+
Hg19::chr8:116215298..116215305,+p@chr8:116215298..116215305
+
Hg19::chr8:116215335..116215378,+p@chr8:116215335..116215378
+
Hg19::chr8:116215608..116215615,+p@chr8:116215608..116215615
+
Hg19::chr8:116342361..116342367,-p@chr8:116342361..116342367
-
Hg19::chr8:39626720..39626725,-p@chr8:39626720..39626725
-
Hg19::chr8:39626962..39626971,-p@chr8:39626962..39626971
-
Hg19::chr8:72268870..72268881,-p14@EYA1
Hg19::chr8:72275738..72275747,-p@chr8:72275738..72275747
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0050789regulation of biological process0.000458795039529669
GO:0065007biological regulation0.000553884666389028
GO:0050794regulation of cellular process0.00127516109800752
GO:0048468cell development0.00278361111199754
GO:0007275multicellular organismal development0.00332281962766397
GO:0050767regulation of neurogenesis0.0035795823346943
GO:0001654eye development0.00470965243789605
GO:0048869cellular developmental process0.00737243277292247
GO:0030154cell differentiation0.00737243277292247
GO:0021902commitment of a neuronal cell to a specific type of neuron in the forebrain0.00850905713084782
GO:0021877forebrain neuron fate commitment0.00850905713084782
GO:0048856anatomical structure development0.00850905713084782
GO:0007423sensory organ development0.00850905713084782
GO:0032502developmental process0.00923177719143751
GO:0021879forebrain neuron differentiation0.00923177719143751
GO:0021872generation of neurons in the forebrain0.00923177719143751
GO:0007435salivary gland morphogenesis0.00923177719143751
GO:0021798forebrain dorsal/ventral pattern formation0.00923177719143751
GO:0022612gland morphogenesis0.00923177719143751
GO:0017034Rap guanyl-nucleotide exchange factor activity0.00923177719143751
GO:0007409axonogenesis0.00923177719143751
GO:0048667neuron morphogenesis during differentiation0.00933276653822271
GO:0048812neurite morphogenesis0.00933276653822271
GO:0000904cellular morphogenesis during differentiation0.00985299067544778
GO:0031175neurite development0.0101773567457619
GO:0032501multicellular organismal process0.0101773567457619
GO:0008046axon guidance receptor activity0.0101773567457619
GO:0046582Rap GTPase activator activity0.0101773567457619
GO:0006366transcription from RNA polymerase II promoter0.011727456069104
GO:0048666neuron development0.011727456069104
GO:0021871forebrain regionalization0.0118716606358403
GO:0007431salivary gland development0.0118716606358403
GO:0005099Ras GTPase activator activity0.0122177020141659
GO:0006916anti-apoptosis0.0125778489838491
GO:0009950dorsal/ventral axis specification0.0131602684796476
GO:0007399nervous system development0.0131602684796476
GO:0048731system development0.0131602684796476
GO:0042462eye photoreceptor cell development0.0149346592481628
GO:0032990cell part morphogenesis0.0149346592481628
GO:0048858cell projection morphogenesis0.0149346592481628
GO:0030030cell projection organization and biogenesis0.0149346592481628
GO:0030182neuron differentiation0.015102049704423
GO:0021543pallium development0.015102049704423
GO:0001754eye photoreceptor cell differentiation0.015102049704423
GO:0043066negative regulation of apoptosis0.0161421034391648
GO:0035272exocrine system development0.0161421034391648
GO:0042461photoreceptor cell development0.0161421034391648
GO:0043069negative regulation of programmed cell death0.0161421034391648
GO:0007417central nervous system development0.0162980930955047
GO:0050793regulation of developmental process0.0162980930955047
GO:0043565sequence-specific DNA binding0.0164439799615083
GO:0048699generation of neurons0.0164605709819633
GO:0046530photoreceptor cell differentiation0.0179020907923902
GO:0022008neurogenesis0.0183074205057291
GO:0045665negative regulation of neuron differentiation0.0183074205057291
GO:0021983pituitary gland development0.0183074205057291
GO:0021537telencephalon development0.0183074205057291
GO:0006355regulation of transcription, DNA-dependent0.0190480001083401
GO:0021536diencephalon development0.0192916008186325
GO:0006351transcription, DNA-dependent0.0199047474675831
GO:0050772positive regulation of axonogenesis0.0199047474675831
GO:0032774RNA biosynthetic process0.0199047474675831
GO:0048663neuron fate commitment0.0210710382746756
GO:0009653anatomical structure morphogenesis0.0219125386674463
GO:0048518positive regulation of biological process0.0224492872519066
GO:0050769positive regulation of neurogenesis0.0229791480795575
GO:0044464cell part0.0233525963137908
GO:0045449regulation of transcription0.0234749276947601
GO:0050679positive regulation of epithelial cell proliferation0.0240942342010499
GO:0009798axis specification0.0240942342010499
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0240942342010499
GO:0005096GTPase activator activity0.0241081661902053
GO:0048523negative regulation of cellular process0.0241679586233096
GO:0006350transcription0.0256288381954396
GO:0010468regulation of gene expression0.0258485786045045
GO:0048519negative regulation of biological process0.0258485786045045
GO:0016524latrotoxin receptor activity0.0280803840498099
GO:0031323regulation of cellular metabolic process0.0280803840498099
GO:0048592eye morphogenesis0.0303769023797294
GO:0050770regulation of axonogenesis0.0303769023797294
GO:0045664regulation of neuron differentiation0.0303769023797294
GO:0009953dorsal/ventral pattern formation0.0323041873562411
GO:0001709cell fate determination0.0325385148482621
GO:0019222regulation of metabolic process0.0325385148482621
GO:0016070RNA metabolic process0.0325385148482621
GO:0050678regulation of epithelial cell proliferation0.0329911108977165
GO:0008047enzyme activator activity0.0334215169677321
GO:0005634nucleus0.0334734779530575
GO:0042127regulation of cell proliferation0.0334734779530575
GO:0050673epithelial cell proliferation0.0334734779530575
GO:0035270endocrine system development0.0334734779530575
GO:0005083small GTPase regulator activity0.0334734779530575
GO:0051056regulation of small GTPase mediated signal transduction0.0334734779530575
GO:0032989cellular structure morphogenesis0.0334734779530575
GO:0000902cell morphogenesis0.0334734779530575
GO:0043010camera-type eye development0.0334734779530575
GO:0010038response to metal ion0.0340972399188216
GO:0001764neuron migration0.0347079612198184
GO:0003700transcription factor activity0.0379919379612352
GO:0010035response to inorganic substance0.0396442858100663
GO:0004364glutathione transferase activity0.0411076048687229
GO:0030900forebrain development0.0421280201981221
GO:0048732gland development0.0421280201981221
GO:0042981regulation of apoptosis0.0429185461111705
GO:0043067regulation of programmed cell death0.0433592482113674
GO:0042221response to chemical stimulus0.0447982881686363
GO:0009952anterior/posterior pattern formation0.0484169636769364
GO:0007411axon guidance0.0488329231328653



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell of lung6.95e-1219
Uber Anatomy
Ontology termp-valuen
respiratory tract epithelium6.95e-1219
lung epithelium6.95e-1219
lung1.80e-1022
respiratory tube1.80e-1022
respiration organ1.80e-1022
pair of lungs1.80e-1022
lung primordium1.80e-1022
lung bud1.80e-1022
respiratory system epithelium1.52e-0828
thoracic cavity element2.74e-0734
thoracic cavity2.74e-0734
thoracic segment organ4.03e-0735
epithelial bud8.21e-0737
Disease
Ontology termp-valuen
lung small cell carcinoma3.10e-504
bronchus cancer1.78e-297
bronchogenic carcinoma1.78e-297
lung carcinoma2.62e-239
lung cancer1.22e-1415
respiratory system cancer8.02e-1416


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.16.73799e-08
MA0004.10.258119
MA0006.10.0188876
MA0007.10.222863
MA0009.10.361827
MA0014.15.12741e-07
MA0017.10.251147
MA0019.10.375902
MA0024.10.068993
MA0025.10.183196
MA0027.11.47809
MA0028.10.113979
MA0029.10.263395
MA0030.10.913628
MA0031.11.13087
MA0038.11.43522
MA0040.11.98297
MA0041.10.47849
MA0042.10.585011
MA0043.10.112621
MA0046.10.107435
MA0048.10.0518
MA0050.10.122838
MA0051.10.743214
MA0052.10.576807
MA0055.10.518243
MA0056.10
MA0057.10.00155878
MA0058.10.106926
MA0059.10.10538
MA0060.18.33684
MA0061.10.0041424
MA0063.10
MA0066.10.0524547
MA0067.10.821067
MA0068.10.00271871
MA0069.10.105679
MA0070.10.677051
MA0071.10.0368616
MA0072.10.325241
MA0073.10.00490845
MA0074.10.281682
MA0076.10.227148
MA0077.12.18872
MA0078.11.13094
MA0081.10.192975
MA0083.11.78662
MA0084.10.448027
MA0087.11.62259
MA0088.10.0194169
MA0089.10
MA0090.10.407981
MA0091.10.263265
MA0092.10.507015
MA0093.10.271319
MA0095.10
MA0098.10
MA0100.10.534027
MA0101.10.0210706
MA0103.10.0813101
MA0105.10.000283017
MA0106.10.188104
MA0107.10.0130823
MA0108.21.57816
MA0109.10
MA0111.10.0835646
MA0113.10.081752
MA0114.10.100555
MA0115.10.251028
MA0116.10.0141277
MA0117.10.130757
MA0119.10.587735
MA0122.10.443081
MA0124.10.636439
MA0125.10.989659
MA0130.10
MA0131.10.282471
MA0132.10
MA0133.10
MA0135.10.399881
MA0136.10.150065
MA0139.10.0543795
MA0140.11.56648
MA0141.10.189342
MA0142.10.365977
MA0143.10.20819
MA0144.10.00826173
MA0145.10.0119239
MA0146.10.00017121
MA0147.10.0349967
MA0148.10.075936
MA0149.14.35946
MA0062.20.231784
MA0035.21.56189
MA0039.20.00663861
MA0138.20.258548
MA0002.20.015813
MA0137.20.123407
MA0104.20.0418155
MA0047.20.17407
MA0112.21.97802e-05
MA0065.20.000857897
MA0150.10.24544
MA0151.10
MA0152.10.636143
MA0153.10.163249
MA0154.10.00359449
MA0155.10.00315375
MA0156.10.216685
MA0157.11.78437
MA0158.10
MA0159.10.197144
MA0160.10.342623
MA0161.10
MA0162.10.000112333
MA0163.19.06078e-07
MA0164.10.223694
MA0080.20.169976
MA0018.20.0732964
MA0099.20.916447
MA0079.27.70271e-12
MA0102.20.478533
MA0258.10.0162526
MA0259.10.0409197
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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

TF#promotersEnrichmentp-valueq-value
CTBP2#148864.090239152564880.003634225134924690.0183723722767994



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C185&oldid=3067303"