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Coexpression cluster:C1580: Difference between revisions

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|tf_chipseq_enrich=BCLAF1#9774;4:17.3221180880975:2.18923511079637e-05:0.000481350580497816!CCNT2#905;4:5.06896126157011:0.00270999809128077:0.0148884529539859!CEBPB#1051;4:6.37691810065985:0.00111394417667732:0.00765238544155773!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298650775282486!E2F6#1876;4:4.01372458535791:0.00663211823393388:0.0282853559389832!EGR1#1958;4:3.99054327584811:0.006780098300144:0.0287544337841606!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00572440244626931!ELK4#2005;5:16.235681658468:8.85705446514576e-07:3.82082573847731e-05!GABPB1#2553;5:7.06768383618217:5.6685482528729e-05:0.000947682905365443!GATA1#2623;4:10.8482465150404:0.000139095691709438:0.00181519616974159!GTF2F1#2962;4:10.1917287014061:0.00017783388942764:0.00215812149406615!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00673506272880161!HMGN3#9324;5:8.17854772335059:2.73180911341838e-05:0.000581192528002245!IRF1#3659;4:6.10973100285112:0.00131552526476799:0.00880549529751358!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130511362655158!NANOG#79923;4:23.3958227848101:6.64263001833934e-06:0.000194382078028955!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00238764252761973!PAX5#5079;4:5.33565242494226:0.00222338958618779:0.0127727494494976!POU2F2#5452;5:9.10612405774252:1.59639992500654e-05:0.000369681622544919!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00247708279302816!SIX5#147912;5:17.086715355459:6.86007756253503e-07:3.09753411393686e-05!SP1#6667;4:4.55870510251272:0.0040757356578168:0.0194750311738449!STAT3#6774;4:8.41557199772339:0.000377152721159863:0.00374139941538896!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135103256923129!TAF7#6879;4:9.14645552393913:0.000272066287241299:0.00290208670954898!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00917641932174204!TFAP2C#7022;4:8.64738288788818:0.000339051887817405:0.00344759420813572!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00136665099035738!USF2#7392;4:10.3937579080557:0.000164617972868753:0.00202574955442909!YY1#7528;5:4.91117074985386:0.0003499314082136:0.0035239115169627!ZEB1#6935;4:13.5107456140351:5.85221769500384e-05:0.000966782290174796!ZNF143#7702;5:13.5008765522279:2.22790360787208e-06:7.97122387470201e-05
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|tfbs_overrepresentation_for_novel_motifs=1.26722,0.205703,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,2.98939,1.50573,0.778743,0.274093,0.721271,0.453496,0.478935,2.21256,0.395009,1.42981,0.501863,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,0.94379,0.27659,4.93661,0.0526856,0.413782,1.57519,1.78381,0.301779,1.06799,0.580638,1.33238,0.451846,0.218848,2.27128,0.734485,1.48156,0.785708,0.458489,1.91222,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,2.15436,1.78554,0.899893,1.32544,1.69665,0.991065,1.53343,2.3794,0.330474,0.554326,1.23387,4.77915,0.255232,1.25519,0.917983,0.987729,1.34093,0.796279,0.934302,0.755403,0.327263,2.6545,0.536557,0.166306,1.88098,0.844289,1.79645,1.41984,2.59889,1.01895,0.367039,2.01367,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,3.91918,0.967698,0.88799,1.49565,0.951411,0.717647,1.35434,0.437618,1.27602,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,4.3389,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,1.63047,0.87256,2.09294,1.41294,0.953361,3.84951,1.87689,1.15522,0.312599,2.9234,1.56426,0.827475,0.439798,0.54968,2.22269,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.923751,0.731946,4.74425
}}
}}

Revision as of 14:59, 26 November 2012


Full id: C1580_acute_Neutrophils_Mallassezderived_migratory_Smooth_Preadipocyte_small



Phase1 CAGE Peaks

Hg19::chr10:44101729..44101736,-p1@CAP1P2
Hg19::chr1:40506327..40506338,+p5@CAP1
Hg19::chr1:40506344..40506355,+p3@CAP1
Hg19::chr1:40506371..40506382,+p2@CAP1
Hg19::chr1:40506393..40506453,+p1@CAP1


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:0007190adenylate cyclase activation0.00508261705718434
GO:0031281positive regulation of cyclase activity0.00508261705718434
GO:0045762positive regulation of adenylate cyclase activity0.00508261705718434
GO:0051349positive regulation of lyase activity0.00508261705718434
GO:0007163establishment and/or maintenance of cell polarity0.00508261705718434
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.00508261705718434
GO:0045761regulation of adenylate cyclase activity0.00508261705718434
GO:0031279regulation of cyclase activity0.00508261705718434
GO:0051339regulation of lyase activity0.00508261705718434
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.00861404579172152
GO:0019933cAMP-mediated signaling0.00861404579172152
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.010221087049063
GO:0019935cyclic-nucleotide-mediated signaling0.010221087049063
GO:0043085positive regulation of catalytic activity0.0194591624475058
GO:0019932second-messenger-mediated signaling0.0194591624475058
GO:0003779actin binding0.0289225113492157
GO:0032989cellular structure morphogenesis0.0289225113492157
GO:0000902cell morphogenesis0.0289225113492157
GO:0008092cytoskeletal protein binding0.03294624985282
GO:0050790regulation of catalytic activity0.03294624985282
GO:0065009regulation of a molecular function0.0339611230639136
GO:0007010cytoskeleton organization and biogenesis0.0339611230639136
GO:0009653anatomical structure morphogenesis0.0495791930950809



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><br>


Cell Type
Ontology termp-valuen
myeloid leukocyte7.56e-2772
monopoietic cell8.45e-2359
monocyte8.45e-2359
monoblast8.45e-2359
promonocyte8.45e-2359
macrophage dendritic cell progenitor9.82e-2361
granulocyte monocyte progenitor cell1.58e-2167
myeloid lineage restricted progenitor cell9.19e-2166
defensive cell1.78e-1948
phagocyte1.78e-1948
somatic cell8.82e-19588
classical monocyte1.02e-1642
CD14-positive, CD16-negative classical monocyte1.02e-1642
somatic stem cell7.33e-15433
multi fate stem cell1.58e-14427
stuff accumulating cell1.80e-1487
myeloid cell2.70e-14108
common myeloid progenitor2.70e-14108
stem cell1.95e-13441
native cell5.44e-12722
animal cell1.32e-11679
eukaryotic cell1.32e-11679
vascular associated smooth muscle cell2.58e-1032
mesenchymal cell2.81e-08354
smooth muscle cell2.98e-0843
smooth muscle myoblast2.98e-0843
connective tissue cell1.58e-07361
muscle precursor cell4.34e-0758
myoblast4.34e-0758
multi-potent skeletal muscle stem cell4.34e-0758
Uber Anatomy
Ontology termp-valuen
mesoderm1.06e-25315
mesoderm-derived structure1.06e-25315
presumptive mesoderm1.06e-25315
lateral plate mesoderm3.53e-23203
musculoskeletal system4.35e-22167
bone marrow7.29e-2076
hemolymphoid system9.71e-20108
hematopoietic system9.85e-2098
blood island9.85e-2098
immune system1.49e-1793
skeletal element2.02e-1790
bone element2.11e-1782
skeletal system7.24e-17100
anatomical system2.72e-11624
anatomical group4.99e-11625
artery2.21e-1042
arterial blood vessel2.21e-1042
arterial system2.21e-1042
cardiovascular system2.90e-10109
circulatory system2.14e-09112
embryonic structure7.27e-09564
epithelial tube open at both ends8.42e-0959
blood vessel8.42e-0959
blood vasculature8.42e-0959
vascular cord8.42e-0959
multi-cellular organism8.69e-09656
vessel1.82e-0868
systemic artery2.20e-0833
systemic arterial system2.20e-0833
splanchnic layer of lateral plate mesoderm2.21e-0883
developing anatomical structure2.36e-08581
vasculature2.92e-0878
vascular system2.92e-0878
germ layer4.34e-08560
germ layer / neural crest4.34e-08560
embryonic tissue4.34e-08560
presumptive structure4.34e-08560
germ layer / neural crest derived structure4.34e-08560
epiblast (generic)4.34e-08560
connective tissue2.96e-07371
embryo7.02e-07592


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)

{{{tfbs_overrepresentation_jaspar}}}



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
BCLAF1#9774417.32211808809752.18923511079637e-050.000481350580497816
CCNT2#90545.068961261570110.002709998091280770.0148884529539859
CEBPB#105146.376918100659850.001113944176677320.00765238544155773
E2F1#186943.925911371903460.007214984547106360.0298650775282486
E2F6#187644.013724585357910.006632118233933880.0282853559389832
EGR1#195843.990543275848110.0067800983001440.0287544337841606
ELF1#199754.258097958807540.0007142416939776840.00572440244626931
ELK4#2005516.2356816584688.85705446514576e-073.82082573847731e-05
GABPB1#255357.067683836182175.6685482528729e-050.000947682905365443
GATA1#2623410.84824651504040.0001390956917094380.00181519616974159
GTF2F1#2962410.19172870140610.000177833889427640.00215812149406615
HEY1#2346254.040111043105710.0009288852205177990.00673506272880161
HMGN3#932458.178547723350592.73180911341838e-050.000581192528002245
IRF1#365946.109731002851120.001315525264767990.00880549529751358
MAX#414956.452555509007128.93743970843928e-050.00130511362655158
NANOG#79923423.39582278481016.64263001833934e-060.000194382078028955
NFKB1#479055.488063424193840.0002008162847462320.00238764252761973
PAX5#507945.335652424942260.002223389586187790.0127727494494976
POU2F2#545259.106124057742521.59639992500654e-050.000369681622544919
SIN3A#2594255.408884726815140.0002159522671657270.00247708279302816
SIX5#147912517.0867153554596.86007756253503e-073.09753411393686e-05
SP1#666744.558705102512720.00407573565781680.0194750311738449
STAT3#677448.415571997723390.0003771527211598630.00374139941538896
TAF1#687253.343046285745290.002394600090870310.0135103256923129
TAF7#687949.146455523939130.0002720662872412990.00290208670954898
TBP#690853.706770687096390.001428755106721120.00917641932174204
TFAP2C#702248.647382887888180.0003390518878174050.00344759420813572
USF1#739156.361499277207969.59569864925045e-050.00136665099035738
USF2#7392410.39375790805570.0001646179728687530.00202574955442909
YY1#752854.911170749853860.00034993140821360.0035239115169627
ZEB1#6935413.51074561403515.85221769500384e-050.000966782290174796
ZNF143#7702513.50087655222792.22790360787208e-067.97122387470201e-05



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


This analysis result is provided for C0 - C305 clusters.