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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1481_CD4_CD8_thymus_CD14CD16_CD14_granulocyte_CD19
|full_id=C1481_CD4_CD8_thymus_CD14CD16_CD14_granulocyte_CD19
|id=C1481
|id=C1481

Revision as of 14:02, 12 September 2012


Full id: C1481_CD4_CD8_thymus_CD14CD16_CD14_granulocyte_CD19



Phase1 CAGE Peaks

Hg19::chr20:52226313..52226350,-p3@ZNF217
Hg19::chr2:182322070..182322155,+p1@ITGA4
Hg19::chr2:182322911..182322927,+p12@ITGA4
Hg19::chr2:182322938..182322962,+p5@ITGA4
Hg19::chr2:182322965..182322977,+p13@ITGA4
Hg19::chr2:182322985..182322998,+p10@ITGA4


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 cell8.64e-56172
angioblastic mesenchymal cell8.64e-56172
hematopoietic cell1.19e-52182
hematopoietic oligopotent progenitor cell1.62e-51165
hematopoietic multipotent progenitor cell1.62e-51165
leukocyte1.56e-44140
hematopoietic lineage restricted progenitor cell1.22e-37124
nongranular leukocyte5.53e-37119
multi fate stem cell3.31e-34430
connective tissue cell9.69e-34365
mesenchymal cell1.81e-33358
stem cell4.28e-33444
somatic stem cell8.04e-33436
motile cell9.63e-29390
myeloid cell2.99e-27112
common myeloid progenitor2.99e-27112
lymphocyte2.36e-2253
common lymphoid progenitor2.36e-2253
lymphoid lineage restricted progenitor cell5.16e-2252
myeloid leukocyte2.61e-1776
myeloid lineage restricted progenitor cell9.56e-1670
granulocyte monocyte progenitor cell1.69e-1571
CD14-positive, CD16-negative classical monocyte4.71e-1542
macrophage dendritic cell progenitor1.03e-1365
monopoietic cell1.40e-1363
monocyte1.40e-1363
monoblast1.40e-1363
promonocyte1.40e-1363
classical monocyte1.10e-1245
mature alpha-beta T cell5.19e-1218
alpha-beta T cell5.19e-1218
immature T cell5.19e-1218
mature T cell5.19e-1218
immature alpha-beta T cell5.19e-1218
T cell1.99e-1125
pro-T cell1.99e-1125
lymphocyte of B lineage4.80e-1024
pro-B cell4.80e-1024
somatic cell2.50e-09591
CD8-positive, alpha-beta T cell9.92e-0911
B cell2.18e-0814
Uber Anatomy
Ontology termp-valuen
connective tissue5.89e-33375
hematopoietic system1.73e-24102
blood island1.73e-24102
hemolymphoid system1.25e-22112
bone element3.96e-1586
bone marrow6.05e-1580
skeletal element4.73e-11101
skeletal system4.73e-11101
immune system2.06e-10115
musculoskeletal system3.07e-10167
blood5.45e-0815
haemolymphatic fluid5.45e-0815
organism substance5.45e-0815
lateral plate mesoderm6.73e-07216
Disease
Ontology termp-valuen
hematologic cancer8.16e-1151
immune system cancer8.16e-1151
leukemia1.62e-0939
myeloid leukemia9.65e-0931


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
CTCF#1066454.466880310895860.001144848346172360.00783633611390057
EBF1#187945.937644564379340.001975153636421710.0114914528791848
EGR1#195854.156815912341780.001617966818864440.0101348789417251
GATA1#2623511.30025678650041.22736455569136e-050.000305274414936533
MAX#414955.377129590839270.000467001558889580.0042949256612248
MYC#460965.22228187160944.92821127172503e-050.000854269638187039
NFKB1#479054.57338618682820.00102196259371130.00724692771079672
POLR2A#543062.147453176558070.01019570676818780.038048646436174
SIN3A#2594243.605923151210090.01273893844487140.0459454360687889
TAF1#687252.785871904787740.01078636340290410.0397978169800006
USF1#739144.240999518138640.007005367750829420.0296088062536978
YY1#752854.092642291544880.001743365462849530.0107267200173525



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.

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