Personal tools

Coexpression cluster:C1900

From FANTOM5_SSTAR

Revision as of 14:17, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1900_Mast_cord_immature_CD14_CD34_chronic_CD4



Phase1 CAGE Peaks

Hg19::chr2:25432921..25432925,-p@chr2:25432921..25432925
-
Hg19::chr2:74758077..74758089,-p@chr2:74758077..74758089
-
Hg19::chr7:37393263..37393284,-p11@ELMO1
Hg19::chr7:37393479..37393526,+p@chr7:37393479..37393526
+
Hg19::chr7:642229..642251,-p@chr7:642229..642251
-


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 cell3.36e-58182
hematopoietic stem cell3.44e-58172
angioblastic mesenchymal cell3.44e-58172
hematopoietic oligopotent progenitor cell1.06e-55165
hematopoietic multipotent progenitor cell1.06e-55165
leukocyte4.65e-51140
hematopoietic lineage restricted progenitor cell1.04e-43124
nongranular leukocyte1.80e-40119
myeloid cell7.05e-34112
common myeloid progenitor7.05e-34112
myeloid leukocyte3.49e-2576
granulocyte monocyte progenitor cell4.38e-2471
myeloid lineage restricted progenitor cell2.41e-2270
macrophage dendritic cell progenitor1.91e-2065
CD14-positive, CD16-negative classical monocyte1.03e-1942
monopoietic cell4.96e-1963
monocyte4.96e-1963
monoblast4.96e-1963
promonocyte4.96e-1963
lymphocyte5.98e-1953
common lymphoid progenitor5.98e-1953
lymphoid lineage restricted progenitor cell8.46e-1952
classical monocyte3.98e-1745
mesenchymal cell9.20e-17358
connective tissue cell1.49e-15365
T cell2.80e-1225
pro-T cell2.80e-1225
motile cell3.29e-12390
mature alpha-beta T cell3.18e-1018
alpha-beta T cell3.18e-1018
immature T cell3.18e-1018
mature T cell3.18e-1018
immature alpha-beta T cell3.18e-1018
stem cell1.68e-09444
multi fate stem cell1.94e-09430
somatic stem cell9.45e-09436
conventional dendritic cell1.38e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.48e-37102
blood island2.48e-37102
hemolymphoid system3.25e-35112
bone marrow6.90e-2480
bone element1.20e-2086
skeletal element4.84e-18101
skeletal system4.84e-18101
immune system2.88e-17115
connective tissue1.27e-14375
blood4.32e-1215
haemolymphatic fluid4.32e-1215
organism substance4.32e-1215
lateral plate mesoderm1.63e-10216
adult organism1.37e-08115
Disease
Ontology termp-valuen
hematologic cancer7.28e-0751
immune system cancer7.28e-0751


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.