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Coexpression cluster:C1505: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;4:5.31409841721654:0.00300804729391746:0.0159827763191619!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438387316737192!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380595260262623!POU2F2#5452;4:6.07074937182835:0.00181532620952452:0.0108947738189019!SMARCC1#6599;2:14.5544531065438:0.00739807938314051:0.0305672355380707!ZEB1#6935;4:11.2589546783626:0.000167270037980545:0.0020487293886068
|tf_chipseq_enrich=CEBPB#1051;4:5.31409841721654:0.00300804729391746:0.0159827763191619!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438387316737192!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380595260262623!POU2F2#5452;4:6.07074937182835:0.00181532620952452:0.0108947738189019!SMARCC1#6599;2:14.5544531065438:0.00739807938314051:0.0305672355380707!ZEB1#6935;4:11.2589546783626:0.000167270037980545:0.0020487293886068
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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.635275,0.650887,1.01544,0.415981,0.889639,0.336106,0.236034,0.127969,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.939587,0.0334022,1.66498,0.585658,0.329602,0.69481,0.936389,0.513952,0.0979105,0.390088,0.992846,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.75612,0.146905,1.15727,0.218784,0.206105,0.562953,0.84426,2.10892,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.406668,1.29353,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.498077,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,2.03545,1.56033,0.483695,0.376529,1.13818,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.840396,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,1.57878,0.949126,1.1919,0.866571,1.07876,0.53374,2.70463,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,2.25278,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.308967,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,1.21528,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.152397
}}
}}

Revision as of 14:56, 26 November 2012


Full id: C1505_immature_CD19_CD4_CD8_Natural_CD14_Peripheral



Phase1 CAGE Peaks

Hg19::chr2:24582702..24582718,+p1@AK096750
Hg19::chr3:105087602..105087625,-p@chr3:105087602..105087625
-
Hg19::chr3:105087786..105087799,+p@chr3:105087786..105087799
+
Hg19::chr3:186285012..186285017,-p@chr3:186285012..186285017
-
Hg19::chr6:26022034..26022042,-p@chr6:26022034..26022042
-
Hg19::chr7:23570219..23570230,+p@chr7:23570219..23570230
+


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
leukocyte1.09e-37136
hematopoietic lineage restricted progenitor cell1.11e-29120
nongranular leukocyte2.66e-29115
hematopoietic stem cell6.16e-29168
angioblastic mesenchymal cell6.16e-29168
hematopoietic cell3.34e-27177
hematopoietic oligopotent progenitor cell1.80e-25161
hematopoietic multipotent progenitor cell1.80e-25161
lymphoid lineage restricted progenitor cell3.78e-2552
lymphocyte1.93e-2453
common lymphoid progenitor1.93e-2453
nucleate cell4.20e-2355
lymphocyte of B lineage1.44e-1324
pro-B cell1.44e-1324
intermediate monocyte9.23e-119
CD14-positive, CD16-positive monocyte9.23e-119
classical monocyte2.23e-1042
CD14-positive, CD16-negative classical monocyte2.23e-1042
CD4-positive, alpha-beta T cell5.48e-106
myeloid leukocyte8.96e-1072
T cell1.56e-0925
pro-T cell1.56e-0925
granulocyte monocyte progenitor cell2.01e-0867
mature alpha-beta T cell2.16e-0818
alpha-beta T cell2.16e-0818
immature T cell2.16e-0818
mature T cell2.16e-0818
immature alpha-beta T cell2.16e-0818
defensive cell2.74e-0848
phagocyte2.74e-0848
macrophage dendritic cell progenitor1.68e-0761
B cell2.88e-0714
myeloid cell5.26e-07108
common myeloid progenitor5.26e-07108
myeloid lineage restricted progenitor cell6.90e-0766
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.63e-0898
blood island5.63e-0898
bone marrow2.85e-0776
hemolymphoid system6.73e-07108


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
CEBPB#105145.314098417216540.003008047293917460.0159827763191619
NFKB1#479043.658708949462560.01207927289015230.0438387316737192
POLR2A#543062.147453176558070.01019570676818780.0380595260262623
POU2F2#545246.070749371828350.001815326209524520.0108947738189019
SMARCC1#6599214.55445310654380.007398079383140510.0305672355380707
ZEB1#6935411.25895467836260.0001672700379805450.0020487293886068



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.