Personal tools

Coexpression cluster:C3607

From FANTOM5_SSTAR

Revision as of 16:33, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3607_Dendritic_CD8_CD4_Macrophage_Monocytederived_chronic_Melanocyte



Phase1 CAGE Peaks

Hg19::chr17:16319065..16319082,+p4@TRPV2
Hg19::chr17:16319083..16319126,+p2@TRPV2
Hg19::chr1:2487631..2487646,+p7@TNFRSF14


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:0005031tumor necrosis factor receptor activity0.0147160534274282
GO:0043120tumor necrosis factor binding0.0147160534274282
GO:0005035death receptor activity0.0147160534274282
GO:0005887integral to plasma membrane0.0213323094237266
GO:0031226intrinsic to plasma membrane0.0213323094237266
GO:0009266response to temperature stimulus0.0213323094237266
GO:0044459plasma membrane part0.0406706632532928
GO:0048770pigment granule0.0406706632532928
GO:0042470melanosome0.0406706632532928
GO:0019955cytokine binding0.0436494179313354
GO:0005262calcium channel activity0.0476836500583188



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 cell3.55e-58172
angioblastic mesenchymal cell3.55e-58172
hematopoietic cell8.67e-58182
hematopoietic oligopotent progenitor cell2.13e-54165
hematopoietic multipotent progenitor cell2.13e-54165
leukocyte2.22e-54140
hematopoietic lineage restricted progenitor cell2.91e-45124
nongranular leukocyte8.22e-45119
connective tissue cell2.21e-33365
mesenchymal cell8.99e-33358
multi fate stem cell2.05e-31430
myeloid cell4.05e-31112
common myeloid progenitor4.05e-31112
somatic stem cell7.95e-29436
stem cell1.23e-28444
motile cell1.15e-27390
myeloid leukocyte1.47e-2676
granulocyte monocyte progenitor cell4.90e-2571
myeloid lineage restricted progenitor cell1.07e-2270
macrophage dendritic cell progenitor2.79e-2265
monopoietic cell1.67e-2163
monocyte1.67e-2163
monoblast1.67e-2163
promonocyte1.67e-2163
lymphocyte1.11e-2053
common lymphoid progenitor1.11e-2053
lymphoid lineage restricted progenitor cell1.23e-2052
CD14-positive, CD16-negative classical monocyte1.09e-1742
classical monocyte1.66e-1445
T cell3.55e-1325
pro-T cell3.55e-1325
mature alpha-beta T cell5.58e-1218
alpha-beta T cell5.58e-1218
immature T cell5.58e-1218
mature T cell5.58e-1218
immature alpha-beta T cell5.58e-1218
somatic cell3.74e-09591
CD8-positive, alpha-beta T cell3.24e-0811
lymphocyte of B lineage1.67e-0724
pro-B cell1.67e-0724
Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.36e-36112
hematopoietic system2.73e-35102
blood island2.73e-35102
connective tissue6.77e-31375
bone marrow1.46e-2580
immune system2.55e-21115
bone element5.83e-2186
lateral plate mesoderm6.82e-20216
skeletal element3.84e-15101
skeletal system3.84e-15101
musculoskeletal system2.36e-12167
blood2.21e-0715
haemolymphatic fluid2.21e-0715
organism substance2.21e-0715
Disease
Ontology termp-valuen
hematologic cancer5.81e-0851
immune system cancer5.81e-0851
leukemia9.73e-0739


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
EGR1#195834.988179094810140.008056488137383440.0320135283103219



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.