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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C756_Eosinophils_Natural_CD8_CD14_CD4_Basophils_Neutrophils
|full_id=C756_Eosinophils_Natural_CD8_CD14_CD4_Basophils_Neutrophils
|gostat_on_coexpression_clusters=GO:0007140!male meiosis!0.012981278700106!11040$GO:0008637!apoptotic mitochondrial changes!0.0176174496644295!11040$GO:0051327!M phase of meiotic cell cycle!0.0235782409042741!11040$GO:0007126!meiosis!0.0235782409042741!11040$GO:0051321!meiotic cell cycle!0.0235782409042741!11040$GO:0008632!apoptotic program!0.0235782409042741!11040$GO:0007005!mitochondrion organization and biogenesis!0.0235782409042741!11040$GO:0006916!anti-apoptosis!0.0394074531967503!11040$GO:0043066!negative regulation of apoptosis!0.0426527728717768!11040$GO:0043069!negative regulation of programmed cell death!0.0426527728717768!11040
|gostat_on_coexpression_clusters=GO:0007140!male meiosis!0.012981278700106!11040$GO:0008637!apoptotic mitochondrial changes!0.0176174496644295!11040$GO:0051327!M phase of meiotic cell cycle!0.0235782409042741!11040$GO:0007126!meiosis!0.0235782409042741!11040$GO:0051321!meiotic cell cycle!0.0235782409042741!11040$GO:0008632!apoptotic program!0.0235782409042741!11040$GO:0007005!mitochondrion organization and biogenesis!0.0235782409042741!11040$GO:0006916!anti-apoptosis!0.0394074531967503!11040$GO:0043066!negative regulation of apoptosis!0.0426527728717768!11040$GO:0043069!negative regulation of programmed cell death!0.0426527728717768!11040

Revision as of 18:28, 12 September 2012


Full id: C756_Eosinophils_Natural_CD8_CD14_CD4_Basophils_Neutrophils



Phase1 CAGE Peaks

Hg19::chr14:35343724..35343735,+p7@ENST00000557373
Hg19::chr14:52313589..52313620,-p@chr14:52313589..52313620
-
Hg19::chr16:31086162..31086174,+p@chr16:31086162..31086174
+
Hg19::chr16:88522520..88522537,-p@chr16:88522520..88522537
-
Hg19::chr17:57696541..57696548,-p@chr17:57696541..57696548
-
Hg19::chr19:13958525..13958536,+p@chr19:13958525..13958536
+
Hg19::chr1:198648829..198648838,-p2@ENST00000455475
Hg19::chr1:53099124..53099132,-p@chr1:53099124..53099132
-
Hg19::chr2:208395615..208395626,-p@chr2:208395615..208395626
-
Hg19::chrX:48776819..48776823,-p5@PIM2
Hg19::chrX:70338312..70338315,-p@chrX:70338312..70338315
-


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:0007140male meiosis0.012981278700106
GO:0008637apoptotic mitochondrial changes0.0176174496644295
GO:0051327M phase of meiotic cell cycle0.0235782409042741
GO:0007126meiosis0.0235782409042741
GO:0051321meiotic cell cycle0.0235782409042741
GO:0008632apoptotic program0.0235782409042741
GO:0007005mitochondrion organization and biogenesis0.0235782409042741
GO:0006916anti-apoptosis0.0394074531967503
GO:0043066negative regulation of apoptosis0.0426527728717768
GO:0043069negative regulation of programmed cell death0.0426527728717768



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
leukocyte1.12e-50140
hematopoietic stem cell2.27e-48172
angioblastic mesenchymal cell2.27e-48172
hematopoietic cell7.30e-46182
hematopoietic oligopotent progenitor cell1.27e-43165
hematopoietic multipotent progenitor cell1.27e-43165
hematopoietic lineage restricted progenitor cell7.40e-40124
nongranular leukocyte2.55e-39119
lymphocyte2.97e-2553
common lymphoid progenitor2.97e-2553
lymphoid lineage restricted progenitor cell5.79e-2552
CD14-positive, CD16-negative classical monocyte6.61e-2242
classical monocyte1.07e-2145
myeloid leukocyte1.82e-1976
myeloid cell6.15e-19112
common myeloid progenitor6.15e-19112
granulocyte monocyte progenitor cell4.05e-1771
myeloid lineage restricted progenitor cell1.94e-1470
macrophage dendritic cell progenitor4.16e-1465
mature alpha-beta T cell8.97e-1418
alpha-beta T cell8.97e-1418
immature T cell8.97e-1418
mature T cell8.97e-1418
immature alpha-beta T cell8.97e-1418
monopoietic cell5.61e-1363
monocyte5.61e-1363
monoblast5.61e-1363
promonocyte5.61e-1363
T cell2.16e-1225
pro-T cell2.16e-1225
lymphocyte of B lineage2.26e-1124
pro-B cell2.26e-1124
mesenchymal cell1.00e-09358
motile cell6.75e-09390
connective tissue cell1.11e-08365
CD8-positive, alpha-beta T cell1.34e-0811
B cell2.79e-0814
intermediate monocyte2.40e-079
CD14-positive, CD16-positive monocyte2.40e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.79e-23102
blood island3.79e-23102
hemolymphoid system5.65e-20112
bone marrow2.15e-1680
bone element5.52e-1586
immune system3.02e-13115
skeletal element6.29e-11101
skeletal system6.29e-11101
connective tissue2.04e-08375


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
E2F1#186973.12288404583230.002204247145175520.0127012064879992
EBF1#187954.048394021167730.004592383252421630.0217044037695566
NFKB1#479073.492403997214260.001102075485228660.0076969146450312



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.