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Coexpression cluster:C4156: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280136820429553!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916850704784147!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321321150454514!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388532456523932!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186953135310146!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295141644262496!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270111751793603!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277416482416014!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190739320728682!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330094785997871
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280136820429553!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916850704784147!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321321150454514!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388532456523932!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186953135310146!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295141644262496!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270111751793603!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277416482416014!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190739320728682!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330094785997871
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}}
}}

Revision as of 16:35, 26 November 2012


Full id: C4156_acute_chronic_Reticulocytes_thymus_CD4_CD34_CD8



Phase1 CAGE Peaks

Hg19::chr2:182322766..182322767,+p22@ITGA4
Hg19::chr2:182322842..182322860,+p7@ITGA4
Hg19::chr2:182322864..182322885,+p3@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 cell7.43e-75168
angioblastic mesenchymal cell7.43e-75168
hematopoietic cell1.26e-70177
hematopoietic oligopotent progenitor cell3.52e-69161
hematopoietic multipotent progenitor cell3.52e-69161
leukocyte4.27e-55136
hematopoietic lineage restricted progenitor cell2.30e-51120
nongranular leukocyte1.37e-49115
myeloid cell7.29e-37108
common myeloid progenitor7.29e-37108
nucleate cell6.98e-3155
lymphocyte6.09e-2953
common lymphoid progenitor6.09e-2953
lymphoid lineage restricted progenitor cell1.84e-2852
mesenchymal cell2.37e-24354
connective tissue cell7.77e-23361
myeloid lineage restricted progenitor cell1.83e-2266
granulocyte monocyte progenitor cell3.22e-2167
myeloid leukocyte1.83e-2072
motile cell4.36e-20386
classical monocyte2.24e-1942
CD14-positive, CD16-negative classical monocyte2.24e-1942
monopoietic cell2.65e-1859
monocyte2.65e-1859
monoblast2.65e-1859
promonocyte2.65e-1859
macrophage dendritic cell progenitor4.67e-1861
defensive cell4.53e-1648
phagocyte4.53e-1648
stem cell2.82e-14441
multi fate stem cell3.48e-14427
lymphocyte of B lineage6.32e-1424
pro-B cell6.32e-1424
T cell8.97e-1425
pro-T cell8.97e-1425
somatic stem cell1.20e-13433
mature alpha-beta T cell6.94e-1318
alpha-beta T cell6.94e-1318
immature T cell6.94e-1318
mature T cell6.94e-1318
immature alpha-beta T cell6.94e-1318
B cell4.88e-1114
CD8-positive, alpha-beta T cell1.51e-1011
intermediate monocyte4.14e-089
CD14-positive, CD16-positive monocyte4.14e-089
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.10e-3098
blood island1.10e-3098
hemolymphoid system4.13e-27108
connective tissue3.15e-21371
immune system6.82e-1993
bone element1.00e-1882
bone marrow1.25e-1876
skeletal element2.63e-1590
skeletal system6.33e-12100
blood1.63e-1015
haemolymphatic fluid1.63e-1015
organism substance1.63e-1015
Disease
Ontology termp-valuen
hematologic cancer2.92e-1751
immune system cancer2.92e-1751
leukemia3.68e-1539
myeloid leukemia1.50e-1431


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#1066435.360256373075030.0064925092527670.0280136820429553
EBF1#187938.9064668465690.00141523283560980.00916850704784147
EGR1#195834.988179094810140.008056488137383440.0321321150454514
GATA1#2623313.56030814380040.0004009615963782630.00388532456523932
MAX#414936.452555509007120.003721913834265510.0186953135310146
MYC#460935.22228187160940.007020843755740150.0295141644262496
NFKB1#479035.488063424193840.006049381815655430.0270111751793603
SIN3A#2594235.408884726815140.006318961977991520.0277416482416014
USF1#739136.361499277207960.00388404057290560.0190739320728682
YY1#752834.911170749853860.008441455341808260.0330094785997871



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.