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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4032_CD4_Dendritic_Natural_CD8_CD19_blood_thymus
|full_id=C4032_CD4_Dendritic_Natural_CD8_CD19_blood_thymus
|id=C4032
|id=C4032

Revision as of 17:04, 12 September 2012


Full id: C4032_CD4_Dendritic_Natural_CD8_CD19_blood_thymus



Phase1 CAGE Peaks

Hg19::chr20:37435934..37435945,-p@chr20:37435934..37435945
-
Hg19::chr9:100864441..100864454,+p@chr9:100864441..100864454
+
Hg19::chr9:100864462..100864485,+p@chr9:100864462..100864485
+


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
lymphocyte6.79e-5053
common lymphoid progenitor6.79e-5053
lymphoid lineage restricted progenitor cell2.01e-4852
leukocyte2.19e-36140
T cell1.29e-3425
pro-T cell1.29e-3425
mature alpha-beta T cell4.08e-3418
alpha-beta T cell4.08e-3418
immature T cell4.08e-3418
mature T cell4.08e-3418
immature alpha-beta T cell4.08e-3418
nongranular leukocyte2.44e-33119
hematopoietic stem cell5.47e-30172
angioblastic mesenchymal cell5.47e-30172
hematopoietic cell2.28e-27182
hematopoietic lineage restricted progenitor cell1.25e-25124
hematopoietic oligopotent progenitor cell4.71e-24165
hematopoietic multipotent progenitor cell4.71e-24165
CD8-positive, alpha-beta T cell7.69e-2111
CD4-positive, alpha-beta T cell1.99e-136
lymphocyte of B lineage5.88e-1224
pro-B cell5.88e-1224
natural killer cell1.00e-073
pro-NK cell1.00e-073
B cell1.02e-0714
plasmacytoid dendritic cell1.05e-073
naive T cell1.70e-073
mononuclear cell6.88e-073
Uber Anatomy
Ontology termp-valuen
thymus8.97e-094
hemolymphoid system gland8.97e-094
thymic region8.97e-094
pharyngeal gland8.97e-094
thymus primordium8.97e-094
hemopoietic organ3.73e-077
blood3.86e-0715
haemolymphatic fluid3.86e-0715
organism substance3.86e-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#53335218.91297006907140.003639406248379680.0183896632238872
IRF4#3662214.60967512449610.006056122473217890.0268415962901207
MEF2A#4205212.4954872730960.008235029478029740.0324881291752332
NFKB1#479035.488063424193840.006049381815655430.0269904044534022
PAX5#507936.669565531177830.003370290999677260.0173112586295821
TCF12#6938310.63446490218640.0008313523990202070.0062985573595409



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.