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Coexpression cluster:C2008: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00353546506185068!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276820333713427!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135571984003038
|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00353546506185068!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276820333713427!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135571984003038
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}}
}}

Revision as of 15:14, 26 November 2012


Full id: C2008_immature_migratory_CD14CD16_CD14_leukemia_mesothelioma_temporal



Phase1 CAGE Peaks

Hg19::chr8:125740643..125740697,-p1@MTSS1
Hg19::chr8:125740699..125740720,-p2@MTSS1
Hg19::chr8:125740730..125740741,-p3@MTSS1
Hg19::chr8:125740876..125740886,-p6@MTSS1
Hg19::chr8:125740895..125740906,-p4@MTSS1


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
classical monocyte4.60e-2242
CD14-positive, CD16-negative classical monocyte4.60e-2242
defensive cell6.08e-2248
phagocyte6.08e-2248
granulocyte monocyte progenitor cell7.49e-2067
myeloid lineage restricted progenitor cell8.29e-1966
macrophage dendritic cell progenitor2.01e-1861
myeloid leukocyte6.95e-1872
monopoietic cell3.38e-1759
monocyte3.38e-1759
monoblast3.38e-1759
promonocyte3.38e-1759
myeloid cell8.16e-14108
common myeloid progenitor8.16e-14108
leukocyte8.86e-14136
hematopoietic lineage restricted progenitor cell2.58e-12120
nongranular leukocyte3.92e-11115
stuff accumulating cell1.02e-1087
hematopoietic oligopotent progenitor cell4.01e-10161
hematopoietic multipotent progenitor cell4.01e-10161
hematopoietic stem cell4.80e-10168
angioblastic mesenchymal cell4.80e-10168
hematopoietic cell3.68e-09177
intermediate monocyte2.16e-079
CD14-positive, CD16-positive monocyte2.16e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.75e-1998
blood island7.75e-1998
hemolymphoid system1.41e-17108
bone marrow3.17e-1676
adult organism7.67e-16114
bone element5.89e-1582
immune system1.26e-1493
skeletal element1.48e-1290
developing anatomical structure1.50e-10581
skeletal system3.16e-10100
embryonic structure4.05e-10564
germ layer6.96e-10560
germ layer / neural crest6.96e-10560
embryonic tissue6.96e-10560
presumptive structure6.96e-10560
germ layer / neural crest derived structure6.96e-10560
epiblast (generic)6.96e-10560
embryo1.12e-09592
tissue3.55e-09773
neural tube5.13e-0956
neural rod5.13e-0956
future spinal cord5.13e-0956
neural keel5.13e-0956
regional part of nervous system1.33e-0853
regional part of brain1.33e-0853
lateral plate mesoderm1.46e-07203
regional part of forebrain2.02e-0741
forebrain2.02e-0741
anterior neural tube2.02e-0741
future forebrain2.02e-0741
anatomical system3.65e-07624
anatomical group5.90e-07625


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
E2F1#186954.907389214879320.0003512818099256460.00353546506185068
MYC#460955.22228187160940.0002573944848850610.00276820333713427
TAF1#687253.343046285745290.002394600090870310.0135571984003038



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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