Personal tools

Coexpression cluster:C3641

From FANTOM5_SSTAR

Revision as of 16:15, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3641_granulocyte_acute_Dendritic_CD133_NK_chronic_biphenotypic



Phase1 CAGE Peaks

Hg19::chr17:4337199..4337254,+p1@SPNS3
Hg19::chr19:55767076..55767090,-p5@PPP6R1
Hg19::chr19:55767125..55767147,-p3@PPP6R1


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 cell8.87e-57168
angioblastic mesenchymal cell8.87e-57168
hematopoietic cell5.10e-52177
hematopoietic oligopotent progenitor cell8.33e-50161
hematopoietic multipotent progenitor cell8.33e-50161
leukocyte5.82e-35136
lymphocyte1.55e-3153
common lymphoid progenitor1.55e-3153
nucleate cell2.51e-3155
lymphoid lineage restricted progenitor cell5.33e-3152
nongranular leukocyte1.07e-30115
hematopoietic lineage restricted progenitor cell3.45e-29120
T cell6.56e-2325
pro-T cell6.56e-2325
myeloid cell9.67e-20108
common myeloid progenitor9.67e-20108
mature alpha-beta T cell3.43e-1618
alpha-beta T cell3.43e-1618
immature T cell3.43e-1618
mature T cell3.43e-1618
immature alpha-beta T cell3.43e-1618
CD8-positive, alpha-beta T cell2.43e-1211
mesenchymal cell4.36e-10354
connective tissue cell2.31e-09361
lymphocyte of B lineage1.18e-0824
pro-B cell1.18e-0824
motile cell6.37e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.23e-1598
blood island5.23e-1598
hemolymphoid system9.21e-14108
blood1.20e-0915
haemolymphatic fluid1.20e-0915
organism substance1.20e-0915
connective tissue2.14e-08371
hemopoietic organ3.09e-087
immune organ3.09e-087
immune system4.40e-0893
Disease
Ontology termp-valuen
hematologic cancer1.97e-3651
immune system cancer1.97e-3651
leukemia8.11e-2939
myeloid leukemia2.85e-2331
lymphoma4.60e-1110


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.