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Coexpression cluster:C2756: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2756_skeletal_Adipocyte_mature_Preadipocyte_Hepatic_Mesenchymal_aorta
|full_id=C2756_skeletal_Adipocyte_mature_Preadipocyte_Hepatic_Mesenchymal_aorta
|id=C2756
|id=C2756

Revision as of 15:32, 12 September 2012


Full id: C2756_skeletal_Adipocyte_mature_Preadipocyte_Hepatic_Mesenchymal_aorta



Phase1 CAGE Peaks

Hg19::chr3:8543500..8543518,+p1@LMCD1
Hg19::chr3:8543533..8543553,+p2@LMCD1
Hg19::chr3:8543561..8543579,+p3@LMCD1
Hg19::chr3:8543591..8543602,+p4@LMCD1


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
non-terminally differentiated cell6.07e-14180
fat cell2.92e-0915
fibroblast9.32e-0875
Uber Anatomy
Ontology termp-valuen
organism subdivision2.63e-17365
trunk1.23e-14216
epithelium1.01e-11309
cell layer1.27e-11312
trunk mesenchyme4.79e-11143
multi-tissue structure1.51e-10347
multi-cellular organism3.16e-10659
compound organ4.02e-1069
mesenchyme1.53e-08238
entire embryonic mesenchyme1.53e-08238
subdivision of trunk1.64e-08113
epithelial tube2.01e-08118
anatomical conduit1.02e-07241
tube1.43e-07194
primary circulatory organ1.71e-0727
anatomical cluster3.27e-07286
somite3.30e-0783
paraxial mesoderm3.30e-0783
presomitic mesoderm3.30e-0783
presumptive segmental plate3.30e-0783
trunk paraxial mesoderm3.30e-0783
presumptive paraxial mesoderm3.30e-0783
adipose tissue3.88e-0714
dermomyotome8.78e-0770
abdominal segment of trunk9.11e-0761
abdomen9.11e-0761


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
CHD2#1106410.34402283411698.73193255208051e-050.00129226909991035
CTCF#1066445.360256373075030.001211145381643620.00818869764442793
E2F1#186944.907389214879320.001724022357361790.0106674074874405
E2F6#187645.017155731697390.00157802193473060.00998406935489968
FOS#235348.99795530889440.0001525147711168630.00195178166654504
HEY1#2346244.040111043105710.00375304636917980.018643664847354
MAFF#23764228.15767824497260.001846876180367150.0109271414797963
MAX#414946.452555509007120.0005767613195645490.00486090828389299
MYC#460945.22228187160940.001344309395272740.00888822036799755
NFYA#4800418.42558069983058.67100748407158e-060.000234913450228003
NFYB#4801416.75979325353651.26678572070404e-050.000311738534129617
NRF1#4899412.21027944771094.49717228915276e-050.000794855604513158
PAX5#507946.669565531177830.0005052774169483260.00444609218541294
RFX5#5993412.04791082719514.74457429336527e-050.000827657582469977
SETDB1#9869440.32002617801053.77887289069054e-071.8528718583607e-05
SP1#666745.69838137814090.0009482606065333980.00685271169981605
SP2#6668426.15353049384462.13562021071447e-067.75528648076526e-05
SRF#6722413.79717826216782.75840773062708e-050.000585182500465084
TAF1#687243.343046285745290.008005664898701650.032294462586153
TCF7L2#6934410.77017656313737.42969445082454e-050.00115623581992201
YY1#752844.911170749853860.00171871838055440.0106992447366467
ZNF263#1012748.221841637010680.0002187871180958320.00249562121306363



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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