Personal tools

Coexpression cluster:C1822

From FANTOM5_SSTAR

Revision as of 11:32, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1822_CD14_CD8_Neutrophils_Natural_Renal_Endothelial_acute



Phase1 CAGE Peaks

Hg19::chr19:41858620..41858632,-p13@TGFB1
Hg19::chr19:41858640..41858665,-p6@TGFB1
Hg19::chr19:41859298..41859309,-p4@TGFB1
Hg19::chr19:41859532..41859555,+p@chr19:41859532..41859555
+
Hg19::chr19:41859814..41859837,-p1@TGFB1


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
somatic cell2.65e-35591
multi fate stem cell4.77e-33430
somatic stem cell2.80e-32436
stem cell5.05e-30444
mesenchymal cell7.81e-28358
connective tissue cell9.32e-28365
native cell2.90e-24722
CD14-positive, CD16-negative classical monocyte2.66e-2242
myeloid leukocyte3.07e-2276
myeloid cell3.01e-21112
common myeloid progenitor3.01e-21112
hematopoietic cell3.50e-21182
hematopoietic stem cell6.02e-21172
angioblastic mesenchymal cell6.02e-21172
hematopoietic oligopotent progenitor cell1.61e-20165
hematopoietic multipotent progenitor cell1.61e-20165
motile cell3.38e-20390
leukocyte1.28e-18140
granulocyte monocyte progenitor cell1.67e-1871
classical monocyte2.65e-1845
macrophage dendritic cell progenitor3.98e-1865
monopoietic cell5.54e-1863
monocyte5.54e-1863
monoblast5.54e-1863
promonocyte5.54e-1863
myeloid lineage restricted progenitor cell2.93e-1770
animal cell3.36e-17679
eukaryotic cell3.36e-17679
nongranular leukocyte7.78e-17119
hematopoietic lineage restricted progenitor cell7.06e-16124
mesodermal cell7.63e-09119
endothelial cell2.03e-0735
vascular associated smooth muscle cell7.53e-0732
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.41e-33216
connective tissue1.28e-25375
hematopoietic system1.40e-19102
blood island1.40e-19102
hemolymphoid system9.11e-19112
bone marrow6.02e-1780
bone element3.04e-1686
musculoskeletal system1.58e-15167
cardiovascular system4.08e-15110
circulatory system4.14e-14113
blood vessel6.61e-1360
epithelial tube open at both ends6.61e-1360
blood vasculature6.61e-1360
vascular cord6.61e-1360
immune system1.12e-12115
splanchnic layer of lateral plate mesoderm1.44e-1284
artery1.52e-1242
arterial blood vessel1.52e-1242
arterial system1.52e-1242
skeletal element1.98e-12101
skeletal system1.98e-12101
vessel1.04e-1169
vasculature1.26e-1179
vascular system1.26e-1179
systemic artery1.17e-0933
systemic arterial system1.17e-0933
epithelial tube9.27e-08118


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
CTCFL#140690311.84788461538460.001201770348538230.00815169795615926
EBF1#187947.12517347725520.0007230531046774210.00577110761936608
GTF2B#2959212.77753197372970.00919936089559720.0347891535132446
NFKB1#479055.488063424193840.0002008162847462320.00239118138896496
RAD21#588536.21302033727380.007751055068811640.0318956832281962
SIN3A#2594244.327107781452110.004977052855762880.0232447197568652
SMC3#912639.02695970695970.002650964449467550.0146395979345358
ZNF143#770238.100525931336740.003624870512090980.018333067865001



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.