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Coexpression cluster:C853: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!1.53e-23!216;UBERON:0002204!5.99e-23!167;UBERON:0002384!1.37e-16!375;UBERON:0002371!1.68e-16!80;UBERON:0004765!1.46e-14!101;UBERON:0001434!1.46e-14!101;UBERON:0002390!2.20e-14!102;UBERON:0003061!2.20e-14!102;UBERON:0002193!2.76e-14!112;UBERON:0001474!1.30e-13!86;UBERON:0000914!1.92e-10!83;UBERON:0002329!1.92e-10!83;UBERON:0003077!1.92e-10!83;UBERON:0003059!1.92e-10!83;UBERON:0007282!1.92e-10!83;UBERON:0009618!1.92e-10!83;UBERON:0007285!1.92e-10!83;UBERON:0001637!2.99e-10!42;UBERON:0003509!2.99e-10!42;UBERON:0004572!2.99e-10!42;UBERON:0000486!3.45e-10!82;UBERON:0002405!5.93e-10!115;UBERON:0004290!1.79e-09!70;UBERON:0000926!2.96e-09!448;UBERON:0004120!2.96e-09!448;UBERON:0006603!2.96e-09!448;UBERON:0004535!1.19e-08!110;UBERON:0004872!1.21e-08!84;UBERON:0001981!2.35e-08!60;UBERON:0007500!2.35e-08!60;UBERON:0004537!2.35e-08!60;UBERON:0006965!2.35e-08!60;UBERON:0004573!4.08e-08!33;UBERON:0004571!4.08e-08!33;UBERON:0001009!5.48e-08!113;UBERON:0000055!7.92e-08!69;UBERON:0001134!1.21e-07!61;UBERON:0002036!1.21e-07!61;UBERON:0003082!1.21e-07!61;UBERON:0002049!2.24e-07!79;UBERON:0007798!2.24e-07!79;UBERON:0002385!4.07e-07!63;UBERON:0001015!4.07e-07!63;UBERON:0000383!4.07e-07!63
|ontology_enrichment_uberon=UBERON:0003081!1.53e-23!216;UBERON:0002204!5.99e-23!167;UBERON:0002384!1.37e-16!375;UBERON:0002371!1.68e-16!80;UBERON:0004765!1.46e-14!101;UBERON:0001434!1.46e-14!101;UBERON:0002390!2.20e-14!102;UBERON:0003061!2.20e-14!102;UBERON:0002193!2.76e-14!112;UBERON:0001474!1.30e-13!86;UBERON:0000914!1.92e-10!83;UBERON:0002329!1.92e-10!83;UBERON:0003077!1.92e-10!83;UBERON:0003059!1.92e-10!83;UBERON:0007282!1.92e-10!83;UBERON:0009618!1.92e-10!83;UBERON:0007285!1.92e-10!83;UBERON:0001637!2.99e-10!42;UBERON:0003509!2.99e-10!42;UBERON:0004572!2.99e-10!42;UBERON:0000486!3.45e-10!82;UBERON:0002405!5.93e-10!115;UBERON:0004290!1.79e-09!70;UBERON:0000926!2.96e-09!448;UBERON:0004120!2.96e-09!448;UBERON:0006603!2.96e-09!448;UBERON:0004535!1.19e-08!110;UBERON:0004872!1.21e-08!84;UBERON:0001981!2.35e-08!60;UBERON:0007500!2.35e-08!60;UBERON:0004537!2.35e-08!60;UBERON:0006965!2.35e-08!60;UBERON:0004573!4.08e-08!33;UBERON:0004571!4.08e-08!33;UBERON:0001009!5.48e-08!113;UBERON:0000055!7.92e-08!69;UBERON:0001134!1.21e-07!61;UBERON:0002036!1.21e-07!61;UBERON:0003082!1.21e-07!61;UBERON:0002049!2.24e-07!79;UBERON:0007798!2.24e-07!79;UBERON:0002385!4.07e-07!63;UBERON:0001015!4.07e-07!63;UBERON:0000383!4.07e-07!63
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13572,0.167775,0.168268,1.78684e-06,0.237199,0.00876024,0.168156,1.16282e-10,0.0824214,0.546774,0.0333049,4.2278e-07,0.503708,0.246187,0.291231,0.198269,0.00104171,0.197483,0.308086,0.20448,1.42224e-08,0.00128849,0.319783,0.139615,0.206257,0.268704,9.14679e-06,0.383259,0.000142318,0.689269,0.675716,4.14603e-09,0.0018739,0.638663,7.61043e-05,0.52491,3.27688e-05,5.31985e-08,0.622646,0.479007,2.91591e-08,0.0846975,0.375599,2.75711e-06,0.536945,0.523194,0.0277872,0.593153,0.000423841,0.336551,0.00157002,0.00178511,0.335207,0.514691,8.23607e-07,0.668131,0.670422,0.249066,0.450988,0.571064,6.02395e-08,0.733696,0.573814,0.539957,0.285349,0.2588,0.000352012,1.48464e-09,0.00291717,0.65176,0.217989,0.650689,0.298817,2.80137e-05,0.475347,2.94055e-05,0.555097,0.000511364,0.536392,0.775775
}}
}}

Revision as of 20:54, 8 August 2012


Full id: C853_Neutrophils_leiomyoma_Smooth_Monocytederived_CD14_Osteoblast_Prostate



Phase1 CAGE Peaks

Hg19::chr1:26607267..26607285,+p@chr1:26607267..26607285
+
Hg19::chr1:26607290..26607307,+p@chr1:26607290..26607307
+
Hg19::chr1:26607342..26607393,+p@chr1:26607342..26607393
+
Hg19::chr1:26607542..26607556,+p@chr1:26607542..26607556
+
Hg19::chr1:26607565..26607584,+p@chr1:26607565..26607584
+
Hg19::chr1:26607589..26607601,+p@chr1:26607589..26607601
+
Hg19::chr1:26607604..26607669,+p@chr1:26607604..26607669
+
Hg19::chr1:26607679..26607701,+p@chr1:26607679..26607701
+
Hg19::chr1:26607704..26607714,+p@chr1:26607704..26607714
+
Hg19::chr1:26607717..26607763,+p@chr1:26607717..26607763
+


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 cell7.89e-32591
somatic stem cell5.32e-28436
multi fate stem cell1.71e-27430
stem cell4.03e-26444
CD14-positive, CD16-negative classical monocyte8.68e-2042
myeloid leukocyte1.78e-1876
connective tissue cell2.10e-17365
classical monocyte8.11e-1745
mesenchymal cell1.01e-16358
myeloid lineage restricted progenitor cell1.22e-1670
native cell4.82e-16722
granulocyte monocyte progenitor cell5.85e-1671
monopoietic cell2.43e-1563
monocyte2.43e-1563
monoblast2.43e-1563
promonocyte2.43e-1563
macrophage dendritic cell progenitor4.69e-1565
animal cell6.61e-15679
eukaryotic cell6.61e-15679
motile cell2.11e-12390
non-terminally differentiated cell3.01e-10180
mesodermal cell4.63e-10119
myeloid cell6.32e-10112
common myeloid progenitor6.32e-10112
muscle precursor cell2.09e-0957
myoblast2.09e-0957
multi-potent skeletal muscle stem cell2.09e-0957
smooth muscle cell5.26e-0942
smooth muscle myoblast5.26e-0942
contractile cell6.32e-0959
muscle cell9.45e-0954
vascular associated smooth muscle cell4.53e-0832
electrically responsive cell9.94e-0860
electrically active cell9.94e-0860
fibroblast2.43e-0775
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.53e-23216
musculoskeletal system5.99e-23167
connective tissue1.37e-16375
bone marrow1.68e-1680
skeletal element1.46e-14101
skeletal system1.46e-14101
hematopoietic system2.20e-14102
blood island2.20e-14102
hemolymphoid system2.76e-14112
bone element1.30e-1386
somite1.92e-1083
paraxial mesoderm1.92e-1083
presomitic mesoderm1.92e-1083
presumptive segmental plate1.92e-1083
trunk paraxial mesoderm1.92e-1083
presumptive paraxial mesoderm1.92e-1083
artery2.99e-1042
arterial blood vessel2.99e-1042
arterial system2.99e-1042
multilaminar epithelium3.45e-1082
immune system5.93e-10115
dermomyotome1.79e-0970
mesoderm2.96e-09448
mesoderm-derived structure2.96e-09448
presumptive mesoderm2.96e-09448
cardiovascular system1.19e-08110
splanchnic layer of lateral plate mesoderm1.21e-0884
blood vessel2.35e-0860
epithelial tube open at both ends2.35e-0860
blood vasculature2.35e-0860
vascular cord2.35e-0860
systemic artery4.08e-0833
systemic arterial system4.08e-0833
circulatory system5.48e-08113
vessel7.92e-0869
skeletal muscle tissue1.21e-0761
striated muscle tissue1.21e-0761
myotome1.21e-0761
vasculature2.24e-0779
vascular system2.24e-0779
muscle tissue4.07e-0763
musculature4.07e-0763
musculature of body4.07e-0763


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)

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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


No analysis results for this cluster

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.