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Coexpression cluster:C4866: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259714999804264!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0402147718223004!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390370838051579
|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259714999804264!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0402147718223004!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390370838051579
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}}
}}

Revision as of 17:00, 26 November 2012


Full id: C4866_melanoma_CD14_Monocytederived_H9_Melanocyte_HES3GFP_iPS



Phase1 CAGE Peaks

Hg19::chrX:15844888..15844904,-p@chrX:15844888..15844904
-
Hg19::chrX:15872889..15872896,-p3@AP1S2
Hg19::chrX:15872914..15872980,-p1@AP1S2


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
monopoietic cell1.30e-3359
monocyte1.30e-3359
monoblast1.30e-3359
promonocyte1.30e-3359
myeloid leukocyte4.33e-3372
myeloid lineage restricted progenitor cell5.70e-3366
macrophage dendritic cell progenitor7.58e-3361
granulocyte monocyte progenitor cell1.83e-3267
defensive cell1.09e-3048
phagocyte1.09e-3048
leukocyte1.85e-29136
nongranular leukocyte1.96e-28115
hematopoietic lineage restricted progenitor cell2.71e-27120
classical monocyte8.03e-2742
CD14-positive, CD16-negative classical monocyte8.03e-2742
hematopoietic stem cell4.17e-23168
angioblastic mesenchymal cell4.17e-23168
hematopoietic oligopotent progenitor cell1.34e-21161
hematopoietic multipotent progenitor cell1.34e-21161
myeloid cell1.91e-21108
common myeloid progenitor1.91e-21108
hematopoietic cell2.09e-20177
stuff accumulating cell1.24e-1987
motile cell1.25e-07386
intermediate monocyte8.48e-079
CD14-positive, CD16-positive monocyte8.48e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.51e-2798
blood island1.51e-2798
bone marrow3.31e-2676
hemolymphoid system4.75e-25108
bone element1.59e-2382
immune system4.87e-2293
skeletal element2.77e-2190
skeletal system1.32e-20100
musculoskeletal system7.49e-11167
nervous system1.43e-0989
central nervous system2.76e-0981
adult organism4.63e-09114
lateral plate mesoderm6.82e-09203
neural tube3.03e-0856
neural rod3.03e-0856
future spinal cord3.03e-0856
neural keel3.03e-0856
brain grey matter4.01e-0834
gray matter4.01e-0834
regional part of forebrain5.59e-0841
forebrain5.59e-0841
anterior neural tube5.59e-0841
future forebrain5.59e-0841
neural plate6.92e-0882
presumptive neural plate6.92e-0882
regional part of nervous system7.27e-0853
regional part of brain7.27e-0853
telencephalon1.16e-0734
regional part of telencephalon1.69e-0732
cerebral hemisphere1.87e-0732
neurectoderm1.95e-0786


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
ATF3#467214.97544968400580.005768294540793880.0259714999804264
ELK4#2005210.8237877723120.01091284719516480.0402147718223004
TFAP2A#7020211.01242291536330.01054990655215560.0390370838051579



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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