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Coexpression cluster:C898: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;3:11.5157009345794:0.00178591501782776:0.0109562487398328!BCLAF1#9774;3:7.21754920337395:0.0067040496194776:0.028501353016715!BRF2#55290;1:119.397286821705:0.00834447063348787:0.0328565890699306!FOXA2#3170;3:8.21015458422175:0.0046728123675689:0.0220535880905838!GATA1#2623;5:7.53350452433358:0.000213260104352918:0.00245835232213184!HDAC2#3066;4:5.962497882945:0.00286427198078623:0.0155228945774134!HEY1#23462;7:3.14230858908222:0.00125876346284377:0.0084586280591906!MAFK#7975;3:9.03357771260997:0.00356785471281375:0.0180832368412868!MEF2A#4205;3:6.24774363654802:0.0100000500846256:0.037498033562696!NFKB1#4790;6:3.65870894946256:0.00185064964860272:0.0109346005120174!PAX5#5079;5:3.70531418398768:0.00561655707771942:0.0253912044255882!POLR2A#5430;9:2.14745317655807:0.00102941289260802:0.00728640142941982!POU2F2#5452;4:4.04716624788557:0.0116142615615323:0.042435693507727!REST#5978;4:4.28890165161245:0.00945702594596283:0.0356654148257831!SIN3A#25942;5:3.00493595934174:0.0140161881734652:0.0491963258829957!SIRT6#51548;3:51.2128013300083:2.24384938017015e-05:0.000490775676263016!STAT1#6772;3:6.90219583239973:0.00759156108216665:0.0312874412162268!STAT2#6773;2:14.5030602636535:0.00786568313225965:0.0322973886632619!TCF7L2#6934;4:4.78674513917215:0.00638205399123472:0.0277827242211897!TRIM28#10155;3:6.19684168175417:0.010227806502978:0.0380840660070064!ZBTB33#10009;3:10.5549083433271:0.00229172162882116:0.0130043529036921!ZEB1#6935;3:5.62947733918129:0.0133048823634195:0.0470363756398743
|tf_chipseq_enrich=BCL3#602;3:11.5157009345794:0.00178591501782776:0.0109562487398328!BCLAF1#9774;3:7.21754920337395:0.0067040496194776:0.028501353016715!BRF2#55290;1:119.397286821705:0.00834447063348787:0.0328565890699306!FOXA2#3170;3:8.21015458422175:0.0046728123675689:0.0220535880905838!GATA1#2623;5:7.53350452433358:0.000213260104352918:0.00245835232213184!HDAC2#3066;4:5.962497882945:0.00286427198078623:0.0155228945774134!HEY1#23462;7:3.14230858908222:0.00125876346284377:0.0084586280591906!MAFK#7975;3:9.03357771260997:0.00356785471281375:0.0180832368412868!MEF2A#4205;3:6.24774363654802:0.0100000500846256:0.037498033562696!NFKB1#4790;6:3.65870894946256:0.00185064964860272:0.0109346005120174!PAX5#5079;5:3.70531418398768:0.00561655707771942:0.0253912044255882!POLR2A#5430;9:2.14745317655807:0.00102941289260802:0.00728640142941982!POU2F2#5452;4:4.04716624788557:0.0116142615615323:0.042435693507727!REST#5978;4:4.28890165161245:0.00945702594596283:0.0356654148257831!SIN3A#25942;5:3.00493595934174:0.0140161881734652:0.0491963258829957!SIRT6#51548;3:51.2128013300083:2.24384938017015e-05:0.000490775676263016!STAT1#6772;3:6.90219583239973:0.00759156108216665:0.0312874412162268!STAT2#6773;2:14.5030602636535:0.00786568313225965:0.0322973886632619!TCF7L2#6934;4:4.78674513917215:0.00638205399123472:0.0277827242211897!TRIM28#10155;3:6.19684168175417:0.010227806502978:0.0380840660070064!ZBTB33#10009;3:10.5549083433271:0.00229172162882116:0.0130043529036921!ZEB1#6935;3:5.62947733918129:0.0133048823634195:0.0470363756398743
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}}
}}

Revision as of 14:33, 26 November 2012


Full id: C898_CD14_Mast_Basophils_Natural_CD19_immature_CD8



Phase1 CAGE Peaks


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




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>



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



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#602311.51570093457940.001785915017827760.0109562487398328
BCLAF1#977437.217549203373950.00670404961947760.028501353016715
BRF2#552901119.3972868217050.008344470633487870.0328565890699306
FOXA2#317038.210154584221750.00467281236756890.0220535880905838
GATA1#262357.533504524333580.0002132601043529180.00245835232213184
HDAC2#306645.9624978829450.002864271980786230.0155228945774134
HEY1#2346273.142308589082220.001258763462843770.0084586280591906
MAFK#797539.033577712609970.003567854712813750.0180832368412868
MEF2A#420536.247743636548020.01000005008462560.037498033562696
NFKB1#479063.658708949462560.001850649648602720.0109346005120174
PAX5#507953.705314183987680.005616557077719420.0253912044255882
POLR2A#543092.147453176558070.001029412892608020.00728640142941982
POU2F2#545244.047166247885570.01161426156153230.042435693507727
REST#597844.288901651612450.009457025945962830.0356654148257831
SIN3A#2594253.004935959341740.01401618817346520.0491963258829957
SIRT6#51548351.21280133000832.24384938017015e-050.000490775676263016
STAT1#677236.902195832399730.007591561082166650.0312874412162268
STAT2#6773214.50306026365350.007865683132259650.0322973886632619
TCF7L2#693444.786745139172150.006382053991234720.0277827242211897
TRIM28#1015536.196841681754170.0102278065029780.0380840660070064
ZBTB33#10009310.55490834332710.002291721628821160.0130043529036921
ZEB1#693535.629477339181290.01330488236341950.0470363756398743



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.