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Coexpression cluster:C1224: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;6:24.3166758030918:1.29931738009616e-08:9.60363820664283e-07!EBF1#1879;6:7.63411443991629:1.2666377582912e-05:0.000312143418683752!MEF2A#4205;6:16.0656264939806:1.53846883349817e-07:8.6292237648612e-06!MEF2C#4208;6:35.4097324222492:1.3745684456669e-09:1.23438137486677e-07!NFKB1#4790;6:4.70405436359472:0.00021611506140197:0.00247786155426066!SP1#6667;6:4.88432689554934:0.000173636112229091:0.00211331801947255
|tf_chipseq_enrich=BCL11A#53335;6:24.3166758030918:1.29931738009616e-08:9.60363820664283e-07!EBF1#1879;6:7.63411443991629:1.2666377582912e-05:0.000312143418683752!MEF2A#4205;6:16.0656264939806:1.53846883349817e-07:8.6292237648612e-06!MEF2C#4208;6:35.4097324222492:1.3745684456669e-09:1.23438137486677e-07!NFKB1#4790;6:4.70405436359472:0.00021611506140197:0.00247786155426066!SP1#6667;6:4.88432689554934:0.000173636112229091:0.00211331801947255
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}}
}}

Revision as of 14:45, 26 November 2012


Full id: C1224_CD4_xeroderma_splenic_CD8_Peripheral_Natural_lymph



Phase1 CAGE Peaks

Hg19::chr16:84801852..84801877,+p@chr16:84801852..84801877
+
Hg19::chr2:242051921..242051933,-p15@PASK
Hg19::chr2:242051966..242051973,-p14@PASK
Hg19::chr2:242051975..242051994,-p2@PASK
Hg19::chr2:242051995..242052016,-p7@PASK
Hg19::chr2:242052022..242052034,-p11@PASK
Hg19::chr2:242052089..242052103,-p9@PASK


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
mature alpha-beta T cell8.23e-4818
alpha-beta T cell8.23e-4818
immature T cell8.23e-4818
mature T cell8.23e-4818
immature alpha-beta T cell8.23e-4818
lymphoid lineage restricted progenitor cell1.19e-3752
T cell3.78e-3725
pro-T cell3.78e-3725
lymphocyte8.49e-3753
common lymphoid progenitor8.49e-3753
nucleate cell3.49e-3555
CD8-positive, alpha-beta T cell6.74e-3311
nongranular leukocyte3.98e-21115
leukocyte2.19e-20136
CD4-positive, alpha-beta T cell1.48e-196
hematopoietic lineage restricted progenitor cell1.33e-15120
hematopoietic stem cell8.90e-15168
angioblastic mesenchymal cell8.90e-15168
hematopoietic cell1.42e-13177
hematopoietic oligopotent progenitor cell1.90e-12161
hematopoietic multipotent progenitor cell1.90e-12161
single nucleate cell1.52e-103
mononuclear cell1.52e-103
naive T cell2.45e-103
natural killer cell3.91e-103
pro-NK cell3.91e-103
regulatory T cell3.52e-072
CD4-positive, CD25-positive, alpha-beta regulatory T cell3.52e-072
naive regulatory T cell3.52e-072
Uber Anatomy
Ontology termp-valuen
hemopoietic organ4.51e-157
immune organ4.51e-157
spleen8.42e-103
gastrointestinal system mesentery8.42e-103
stomach region8.42e-103
mesentery8.42e-103
gastrointestinal system serosa8.42e-103
mesentery of stomach8.42e-103
gut mesentery8.42e-103
dorsal mesentery8.42e-103
dorsal mesogastrium8.42e-103
peritoneal cavity8.42e-103
spleen primordium8.42e-103
thymus2.66e-074
hemolymphoid system gland2.66e-074
thymic region2.66e-074
pharyngeal gland2.66e-074
thymus primordium2.66e-074
blood5.77e-0715
haemolymphatic fluid5.77e-0715
organism substance5.77e-0715


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
BCL11A#53335624.31667580309181.29931738009616e-089.60363820664283e-07
EBF1#187967.634114439916291.2666377582912e-050.000312143418683752
MEF2A#4205616.06562649398061.53846883349817e-078.6292237648612e-06
MEF2C#4208635.40973242224921.3745684456669e-091.23438137486677e-07
NFKB1#479064.704054363594720.000216115061401970.00247786155426066
SP1#666764.884326895549340.0001736361122290910.00211331801947255



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.