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Coexpression cluster:C2695: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127495413179632!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512982518194801!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.0012920860070937!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818551818504357!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199845497828406!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101565716900369!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161139293138856!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.00154677183007077!FOSL1#8061;3:29.7851847872798:6.26173959487248e-05:0.00102519175662155!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390659272632087!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.00062763069717631!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248404774812856!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.0030788541730125!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485894776591126!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142569662743404!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00888597018562591!NFE2#4778;4:77.204260651629:2.80776035215453e-08:1.91785273655112e-06!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768544668881108!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444496867829062!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797351517580686!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00685034166740967!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281071960124646!STAT1#6772;4:20.7065874971992:5.43610708103893e-06:0.000165522328698724!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115589134328864!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000230573208781102!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508535081763335!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000681940271852044!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342534483736442!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304861394729375!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000621486237705785
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|tfbs_overrepresentation_for_novel_motifs=1.44014,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,2.01638,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,1.67497,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,1.53358,1.72987,1.33003,0.806311,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,2.0411,0.371755,0.493145,0.66492,3.90795,0.53106,0.0946706,0.61613,0.822818,0.694903,1.57574,0.538016,0.90714,0.83543,1.29278,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.72726,1.18341,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,2.16273,2.11025,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,2.02143,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,3.6853,1.811,0.963351,2.1895,0.661255,0.437774,1.91548,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,1.28873,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,2.28137,0.843324,0.423521,0.820225,1.4289
}}
}}

Revision as of 15:39, 26 November 2012


Full id: C2695_neuroectodermal_Dendritic_thymus_acute_granulocyte_CD19_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr2:242824077..242824114,+p1@ENST00000429947
Hg19::chr2:242824118..242824127,+p4@ENST00000429947
Hg19::chr2:242824129..242824140,+p5@ENST00000429947
Hg19::chr2:242824142..242824158,+p2@ENST00000429947


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


No GOStat results

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>


Uber Anatomy
Ontology termp-valuen
sympathetic nervous system5.30e-085
autonomic nervous system5.30e-085
Disease
Ontology termp-valuen
neuroectodermal tumor4.16e-1510
germ cell and embryonal cancer4.78e-0922
germ cell cancer4.78e-0922
neuroendocrine tumor4.98e-096


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
ATF3#467422.46317452600873.92475754624726e-060.000127495413179632
CCNT2#90546.336201576962630.0006203100587215640.00512982518194801
CHD2#1106410.34402283411698.73193255208051e-050.0012920860070937
CTCF#1066445.360256373075030.001211145381643620.00818551818504357
EBF1#187948.9064668465690.00015887907472010.00199845497828406
EGR1#195844.988179094810140.001615011500076050.0101565716900369
ELF1#199744.258097958807540.003041525565781240.0161139293138856
ETS1#211349.728760922202340.0001115955317418140.00154677183007077
FOSL1#8061329.78518478727986.26173959487248e-050.00102519175662155
GABPB1#255347.067683836182170.0004006876864423170.00390659272632087
HDAC2#3066413.41562023662633.0859005065161e-050.00062763069717631
HMGN3#932448.178547723350590.0002234570284440470.00248404774812856
IRF1#365947.63716375356390.0002938853996185490.0030788541730125
MAX#414946.452555509007120.0005767613195645490.00485894776591126
MXI1#460149.96157162875930.0001015224754950450.00142569662743404
MYC#460945.22228187160940.001344309395272740.00888597018562591
NFE2#4778477.2042606516292.80776035215453e-081.91785273655112e-06
NFKB1#479045.488063424193840.001102199566301980.00768544668881108
PAX5#507946.669565531177830.0005052774169483260.00444496867829062
SIN3A#2594245.408884726815140.001168172384885160.00797351517580686
SP1#666745.69838137814090.0009482606065333980.00685034166740967
SPI1#668836.153242631392040.006580387113059030.0281071960124646
STAT1#6772420.70658749719925.43610708103893e-060.000165522328698724
TCF7L2#6934410.77017656313737.42969445082454e-050.00115589134328864
TRIM28#10155418.59052504526258.36730015875654e-060.000230573208781102
USF1#739146.361499277207960.0006105011399140830.00508535081763335
USF2#7392412.99219738506963.50833029870167e-050.000681940271852044
ZBTB7A#5134135.513931980906920.009038352821081090.0342534483736442
ZEB1#6935416.88843201754391.22862303393937e-050.000304861394729375
ZNF143#7702413.50087655222793.00867915035614e-050.000621486237705785



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.