Personal tools

Coexpression cluster:C1656

From FANTOM5_SSTAR

Revision as of 11:33, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1656_CD14CD16_CD14_CD4_Basophils_CD8_Natural_immature



Phase1 CAGE Peaks

Hg19::chr12:109025991..109025997,+p@chr12:109025991..109025997
+
Hg19::chr17:76835866..76835913,+p@chr17:76835866..76835913
+
Hg19::chr17:76836459..76836475,+p@chr17:76836459..76836475
+
Hg19::chr1:245134406..245134424,+p@chr1:245134406..245134424
+
Hg19::chr1:6663744..6663762,-p3@KLHL21


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><br>


Cell Type
Ontology termp-valuen
leukocyte2.64e-60136
hematopoietic lineage restricted progenitor cell6.05e-50120
nongranular leukocyte7.84e-49115
hematopoietic stem cell7.15e-47168
angioblastic mesenchymal cell7.15e-47168
hematopoietic cell1.14e-44177
hematopoietic oligopotent progenitor cell2.90e-42161
hematopoietic multipotent progenitor cell2.90e-42161
classical monocyte3.52e-4142
CD14-positive, CD16-negative classical monocyte3.52e-4142
defensive cell1.51e-3548
phagocyte1.51e-3548
myeloid leukocyte8.13e-3572
granulocyte monocyte progenitor cell2.63e-3367
macrophage dendritic cell progenitor8.47e-3061
myeloid lineage restricted progenitor cell5.73e-2966
monopoietic cell6.89e-2859
monocyte6.89e-2859
monoblast6.89e-2859
promonocyte6.89e-2859
myeloid cell1.74e-23108
common myeloid progenitor1.74e-23108
lymphoid lineage restricted progenitor cell6.52e-1852
lymphocyte2.44e-1753
common lymphoid progenitor2.44e-1753
nucleate cell2.92e-1655
mature alpha-beta T cell2.32e-1418
alpha-beta T cell2.32e-1418
immature T cell2.32e-1418
mature T cell2.32e-1418
immature alpha-beta T cell2.32e-1418
mesenchymal cell2.34e-14354
T cell2.94e-1425
pro-T cell2.94e-1425
connective tissue cell2.02e-13361
stuff accumulating cell2.16e-1387
intermediate monocyte3.86e-129
CD14-positive, CD16-positive monocyte3.86e-129
motile cell8.92e-12386
CD4-positive, alpha-beta T cell3.06e-086
multi fate stem cell7.33e-08427
stem cell9.24e-08441
CD8-positive, alpha-beta T cell1.39e-0711
somatic stem cell2.41e-07433
Uber Anatomy
Ontology termp-valuen
bone marrow8.38e-3076
bone element1.83e-2782
hematopoietic system1.40e-2698
blood island1.40e-2698
skeletal element2.69e-2390
immune system3.96e-2393
hemolymphoid system3.61e-22108
skeletal system4.31e-19100
connective tissue1.52e-12371


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
HDAC8#558691155.3168067226890.006421962435230970.0279285169591125
MXI1#460135.976942977255580.008653004889366880.0329412837224097
MYC#460944.177825497287520.005691969036823440.0256699004334055
SIN3A#2594244.327107781452110.004977052855762880.0232384845852566



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.