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Coexpression cluster:C2572: Difference between revisions

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|tf_chipseq_enrich=NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000234669953518775
|tf_chipseq_enrich=NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000234669953518775
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}}
}}

Revision as of 15:35, 26 November 2012


Full id: C2572_NK_chronic_embryonic_lymphoma_epithelioid_acute_adult



Phase1 CAGE Peaks

Hg19::chr1:226613592..226613598,-p@chr1:226613592..226613598
-
Hg19::chr2:26139327..26139333,+p@chr2:26139327..26139333
+
Hg19::chr6:2940610..2940615,+p@chr6:2940610..2940615
+
Hg19::chr6:3028692..3028697,+p@chr6:3028692..3028697
+


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell2.52e-34168
angioblastic mesenchymal cell2.52e-34168
hematopoietic cell1.29e-32177
hematopoietic oligopotent progenitor cell2.26e-31161
hematopoietic multipotent progenitor cell2.26e-31161
leukocyte6.77e-18136
myeloid cell3.20e-17108
common myeloid progenitor3.20e-17108
hematopoietic lineage restricted progenitor cell7.39e-15120
nucleate cell4.79e-1455
lymphocyte1.23e-1353
common lymphoid progenitor1.23e-1353
lymphoid lineage restricted progenitor cell1.03e-1252
nongranular leukocyte1.47e-12115
T cell7.65e-1025
pro-T cell7.65e-1025
motile cell1.49e-08386
histamine secreting cell9.49e-085
biogenic amine secreting cell9.49e-085
granulocytopoietic cell9.49e-085
mast cell9.49e-085
mast cell progenitor9.49e-085
basophil mast progenitor cell9.49e-085
mesenchymal cell1.16e-07354
connective tissue cell3.63e-07361
Uber Anatomy
Ontology termp-valuen
connective tissue1.04e-07371
Disease
Ontology termp-valuen
hematologic cancer5.26e-3651
immune system cancer5.26e-3651
leukemia1.75e-2939
myeloid leukemia6.98e-1931
chronic leukemia8.86e-148
lymphoma1.55e-1210
cancer2.56e-12235
organ system cancer4.10e-12137
disease of cellular proliferation1.05e-11239


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)

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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
NFYA#4800418.42558069983058.67100748407158e-060.000234669953518775



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.