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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1020_Mast_CD4_acute_chronic_CD8_thymus_Peripheral
|full_id=C1020_Mast_CD4_acute_chronic_CD8_thymus_Peripheral
|id=C1020
|id=C1020

Revision as of 13:26, 12 September 2012


Full id: C1020_Mast_CD4_acute_chronic_CD8_thymus_Peripheral



Phase1 CAGE Peaks

Hg19::chr12:55378459..55378469,-p4@KIAA0748
Hg19::chr12:55378470..55378554,-p1@KIAA0748
Hg19::chr16:30671223..30671261,+p4@FBRS
Hg19::chr2:196521610..196521660,+p5@SLC39A10
Hg19::chrX:135861719..135861749,-p@chrX:135861719..135861749
-
Hg19::chrX:135863036..135863078,-p1@ARHGEF6
Hg19::chrX:135863084..135863115,-p2@ARHGEF6
Hg19::chrX:135863137..135863146,-p11@ARHGEF6


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 cell6.08e-65172
angioblastic mesenchymal cell6.08e-65172
hematopoietic cell3.62e-62182
hematopoietic oligopotent progenitor cell1.11e-60165
hematopoietic multipotent progenitor cell1.11e-60165
leukocyte5.82e-52140
hematopoietic lineage restricted progenitor cell1.61e-43124
nongranular leukocyte4.29e-41119
myeloid cell1.71e-32112
common myeloid progenitor1.71e-32112
lymphocyte1.88e-2553
common lymphoid progenitor1.88e-2553
lymphoid lineage restricted progenitor cell5.28e-2552
myeloid leukocyte5.67e-2176
mesenchymal cell2.63e-19358
connective tissue cell1.16e-18365
granulocyte monocyte progenitor cell2.95e-1871
myeloid lineage restricted progenitor cell6.70e-1870
multi fate stem cell1.06e-15430
macrophage dendritic cell progenitor5.06e-1565
T cell7.43e-1525
pro-T cell7.43e-1525
monopoietic cell1.66e-1463
monocyte1.66e-1463
monoblast1.66e-1463
promonocyte1.66e-1463
somatic stem cell3.37e-14436
stem cell1.39e-13444
CD14-positive, CD16-negative classical monocyte2.59e-1342
motile cell3.34e-12390
mature alpha-beta T cell7.26e-1218
alpha-beta T cell7.26e-1218
immature T cell7.26e-1218
mature T cell7.26e-1218
immature alpha-beta T cell7.26e-1218
classical monocyte4.83e-1145
lymphocyte of B lineage6.38e-1024
pro-B cell6.38e-1024
CD8-positive, alpha-beta T cell8.52e-0811
B cell2.27e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.72e-27102
blood island7.72e-27102
hemolymphoid system2.39e-26112
connective tissue1.90e-18375
bone marrow7.99e-1780
bone element8.03e-1586
immune system3.29e-13115
adult organism3.10e-11115
skeletal element6.19e-11101
skeletal system6.19e-11101
blood1.81e-0815
haemolymphatic fluid1.81e-0815
organism substance1.81e-0815
musculoskeletal system3.82e-08167
lateral plate mesoderm5.87e-08216
Disease
Ontology termp-valuen
hematologic cancer6.09e-1651
immune system cancer6.09e-1651
leukemia2.53e-1439
myeloid leukemia1.25e-1031


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
POLR2A#543082.147453176558070.002210725788971910.0127153866435971



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.