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Coexpression cluster:C4482: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000527851931482102!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280879488774174!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435397362211776!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000253998323974766!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187214255616652!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0072230408108411!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295641440611945!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270562882722469!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00200129105876023!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246517588461854!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.0088497145042893!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667327050344922!REST#5978;3:9.65002871612802:0.00111263624711459:0.00770318972571433!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486042702685059!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027790713354085!SIRT6#51548;3:153.638403990025:2.75057764221434e-07:1.40473143459767e-05!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310370149891909!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247580479296419!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644800059784391!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544892705304875!USF2#7392;3:12.9921973850696:0.000455897939342781:0.004225927477325!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109909534098961
|tf_chipseq_enrich=BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000527851931482102!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280879488774174!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435397362211776!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000253998323974766!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187214255616652!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0072230408108411!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295641440611945!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270562882722469!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00200129105876023!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246517588461854!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.0088497145042893!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667327050344922!REST#5978;3:9.65002871612802:0.00111263624711459:0.00770318972571433!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486042702685059!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027790713354085!SIRT6#51548;3:153.638403990025:2.75057764221434e-07:1.40473143459767e-05!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310370149891909!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247580479296419!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644800059784391!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544892705304875!USF2#7392;3:12.9921973850696:0.000455897939342781:0.004225927477325!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109909534098961
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,1.65118,0.242883,0.845342,2.6017,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,1.54087,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,2.06667,0.388177,0.891404,1.25741,2.16722,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,2.15606,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,2.35823,0.450952,1.27663,1.05794,1.68795,2.38768,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,1.67826,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,3.2678,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,3.03644,2.09999,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:46, 26 November 2012


Full id: C4482_Dendritic_iPS_anaplastic_H9_chronic_acute_Endothelial



Phase1 CAGE Peaks

Hg19::chr5:162930253..162930275,+p4@MAT2B
Hg19::chr5:162930283..162930303,+p3@MAT2B
Hg19::chr5:162930308..162930345,+p2@MAT2B


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><br><br>disease_data<br>

Disease
Ontology termp-valuen
leukemia5.15e-1139
myeloid leukemia2.03e-0931
hematologic cancer4.14e-0851
immune system cancer4.14e-0851


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
BCL3#602334.54710280373832.42397750207122e-050.000527851931482102
CTCF#1066435.360256373075030.0064925092527670.0280879488774174
GTF2F1#2962312.73966087675770.0004835525047438590.00435397362211776
IRF3#3661346.98195221148969.63568551583244e-060.000253998323974766
MAX#414936.452555509007120.003721913834265510.0187214255616652
MXI1#460139.96157162875930.001011470541259020.0072230408108411
MYC#460935.22228187160940.007020843755740150.0295641440611945
NFKB1#479035.488063424193840.006049381815655430.0270562882722469
NFYA#4800318.42558069983050.0001598135507814160.00200129105876023
NFYB#4801316.75979325353650.0002123649923296180.00246517588461854
POU2F2#545239.106124057742520.001324165192682130.0088497145042893
RAD21#5885310.35503389545630.0009004912073565420.00667327050344922
REST#597839.650028716128020.001112636247114590.00770318972571433
RFX5#5993312.04791082719510.0005717246050312580.00486042702685059
SIN3A#2594235.408884726815140.006318961977991520.027790713354085
SIRT6#515483153.6384039900252.75057764221434e-071.40473143459767e-05
SMC3#9126315.04493284493280.0002935825420371870.00310370149891909
SP1#666735.69838137814090.005403962701712170.0247580479296419
STAT3#6774310.51946499715420.0008589184530415310.00644800059784391
TAF7#6879311.43306940492390.0006690181981945830.00544892705304875
USF2#7392312.99219738506960.0004558979393427810.004225927477325
ZNF263#1012738.221841637010680.001799043925565870.0109909534098961



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.

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