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Coexpression cluster:C2801: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:18.2683513442277:0.000268166010572129:0.00286809933211906!BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296302825432056!BCL3#602;2:17.2735514018692:0.00483449420807607:0.022679321771426!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240609026982594!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00366028410239091!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.00488945176176339!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00769006750651428!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.04351897204998!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227735765189997!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281117948910203
|tf_chipseq_enrich=BATF#10538;3:18.2683513442277:0.000268166010572129:0.00286809933211906!BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296302825432056!BCL3#602;2:17.2735514018692:0.00483449420807607:0.022679321771426!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240609026982594!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00366028410239091!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.00488945176176339!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00769006750651428!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.04351897204998!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227735765189997!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281117948910203
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}}
}}

Revision as of 15:43, 26 November 2012


Full id: C2801_Natural_B_CD8_xeroderma_CD34_plasma_Basophils



Phase1 CAGE Peaks

Hg19::chr5:133468482..133468495,+p@chr5:133468482..133468495
+
Hg19::chr8:101507517..101507549,-p@chr8:101507517..101507549
-
Hg19::chr9:116279713..116279734,+p15@RGS3
Hg19::chrX:53741792..53741809,-p@chrX:53741792..53741809
-


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><br>


Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell9.91e-5352
lymphocyte1.74e-5153
common lymphoid progenitor1.74e-5153
nucleate cell3.92e-4955
T cell1.25e-3325
pro-T cell1.25e-3325
leukocyte3.68e-32136
mature alpha-beta T cell9.88e-3018
alpha-beta T cell9.88e-3018
immature T cell9.88e-3018
mature T cell9.88e-3018
immature alpha-beta T cell9.88e-3018
nongranular leukocyte1.18e-29115
hematopoietic lineage restricted progenitor cell3.90e-26120
hematopoietic cell5.67e-25177
hematopoietic stem cell5.76e-24168
angioblastic mesenchymal cell5.76e-24168
hematopoietic oligopotent progenitor cell4.45e-21161
hematopoietic multipotent progenitor cell4.45e-21161
CD8-positive, alpha-beta T cell1.71e-1711
lymphocyte of B lineage1.11e-1524
pro-B cell1.11e-1524
CD4-positive, alpha-beta T cell2.68e-126
circulating cell1.92e-106
natural killer cell9.57e-083
pro-NK cell9.57e-083
basophil2.71e-073
Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.96e-127
immune organ2.96e-127
blood1.02e-1015
haemolymphatic fluid1.02e-1015
organism substance1.02e-1015
thymus1.19e-074
hemolymphoid system gland1.19e-074
thymic region1.19e-074
pharyngeal gland1.19e-074
thymus primordium1.19e-074


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
BATF#10538318.26835134422770.0002681660105721290.00286809933211906
BCL11A#53335214.18472755180350.007108328585298740.0296302825432056
BCL3#602217.27355140186920.004834494208076070.022679321771426
EBF1#187936.679850134926750.005184294118278910.0240609026982594
IRF4#3662316.43588451505810.0003669431395554610.00366028410239091
MEF2A#4205314.0574231822330.0005830038854186610.00488945176176339
NFKB1#479045.488063424193840.001102199566301980.00769006750651428
PAX5#507935.002174148383370.01196533174786410.04351897204998
POU2F2#545236.829593043306890.004860473775203740.0227735765189997
SPI1#668836.153242631392040.006580387113059030.0281117948910203



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.