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Coexpression cluster:C1178: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0007050!cell cycle arrest!0.0401565995525727!10669$GO:0008285!negative regulation of cell proliferation!0.0401565995525727!10669$GO:0045786!negative regulation of progression through cell cycle!0.0401565995525727!10669$GO:0000074!regulation of progression through cell cycle!0.0401565995525727!10669$GO:0051726!regulation of cell cycle!0.0401565995525727!10669$GO:0042127!regulation of cell proliferation!0.043717375093214!10669$GO:0022402!cell cycle process!0.0499360818152764!10669
|gostat_on_coexpression_clusters=GO:0007050!cell cycle arrest!0.0401565995525727!10669$GO:0008285!negative regulation of cell proliferation!0.0401565995525727!10669$GO:0045786!negative regulation of progression through cell cycle!0.0401565995525727!10669$GO:0000074!regulation of progression through cell cycle!0.0401565995525727!10669$GO:0051726!regulation of cell cycle!0.0401565995525727!10669$GO:0042127!regulation of cell proliferation!0.043717375093214!10669$GO:0022402!cell cycle process!0.0499360818152764!10669
|id=C1178
|id=C1178
|ontology_enrichment_celltype=CL:0000084!1.64e-10!25;CL:0000827!1.64e-10!25;CL:0000791!6.88e-09!18;CL:0000789!6.88e-09!18;CL:0002420!6.88e-09!18;CL:0002419!6.88e-09!18;CL:0000790!6.88e-09!18;CL:0000838!2.84e-08!52;CL:0000542!7.01e-08!53;CL:0000051!7.01e-08!53
|ontology_enrichment_disease=DOID:162!3.19e-14!235;DOID:14566!4.56e-13!239;DOID:2531!1.32e-10!51;DOID:0060083!1.32e-10!51;DOID:0050687!5.03e-09!143;DOID:305!1.50e-08!106;DOID:1240!1.65e-08!39;DOID:0050686!1.98e-07!137
|ontology_enrichment_uberon=
}}
}}

Revision as of 14:08, 21 May 2012


Full id: C1178_embryonic_testicular_teratocarcinoma_lymphangiectasia_epithelioid_bronchioalveolar_testis



Phase1 CAGE Peaks

Hg19::chr12:8034651..8034657,+p2@NANOGP1
Hg19::chr15:70878941..70878946,-p1@ENST00000513467
Hg19::chr19:13296953..13296959,-p@chr19:13296953..13296959
-
Hg19::chr1:113396682..113396688,-p@chr1:113396682..113396688
-
Hg19::chr1:37984640..37984646,+p@chr1:37984640..37984646
+
Hg19::chr2:27333965..27333971,-p6@CGREF1
Hg19::chr4:2764467..2764473,-p@chr4:2764467..2764473
-


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


GO IDGO nameFDR corrected p-value
GO:0007050cell cycle arrest0.0401565995525727
GO:0008285negative regulation of cell proliferation0.0401565995525727
GO:0045786negative regulation of progression through cell cycle0.0401565995525727
GO:0000074regulation of progression through cell cycle0.0401565995525727
GO:0051726regulation of cell cycle0.0401565995525727
GO:0042127regulation of cell proliferation0.043717375093214
GO:0022402cell cycle process0.0499360818152764



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><br>disease_data<br>


Cell Type
Ontology termp-valuen
T cell1.64e-1025
pro-T cell1.64e-1025
mature alpha-beta T cell6.88e-0918
alpha-beta T cell6.88e-0918
immature T cell6.88e-0918
mature T cell6.88e-0918
immature alpha-beta T cell6.88e-0918
lymphoid lineage restricted progenitor cell2.84e-0852
lymphocyte7.01e-0853
common lymphoid progenitor7.01e-0853
Disease
Ontology termp-valuen
cancer3.19e-14235
disease of cellular proliferation4.56e-13239
hematologic cancer1.32e-1051
immune system cancer1.32e-1051
cell type cancer5.03e-09143
carcinoma1.50e-08106
leukemia1.65e-0839
organ system cancer1.98e-07137


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


No analysis results for this cluster

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.