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Coexpression cluster:C4734: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002204!4.08e-23!167;UBERON:0000926!7.61e-20!448;UBERON:0004120!7.61e-20!448;UBERON:0006603!7.61e-20!448;UBERON:0003081!4.22e-16!216;UBERON:0000914!5.94e-15!83;UBERON:0002329!5.94e-15!83;UBERON:0003077!5.94e-15!83;UBERON:0003059!5.94e-15!83;UBERON:0007282!5.94e-15!83;UBERON:0009618!5.94e-15!83;UBERON:0007285!5.94e-15!83;UBERON:0000468!3.61e-14!659;UBERON:0000480!2.41e-13!626;UBERON:0004290!2.41e-13!70;UBERON:0000467!2.64e-13!625;UBERON:0000486!7.73e-13!82;UBERON:0004765!3.09e-12!101;UBERON:0001434!3.09e-12!101;UBERON:0002384!1.33e-10!375;UBERON:0003102!2.09e-10!95;UBERON:0001134!3.01e-10!61;UBERON:0002036!3.01e-10!61;UBERON:0003082!3.01e-10!61;UBERON:0001474!3.32e-10!86;UBERON:0004872!4.06e-10!84;UBERON:0000923!5.64e-10!604;UBERON:0005291!5.64e-10!604;UBERON:0006598!5.64e-10!604;UBERON:0002532!5.64e-10!604;UBERON:0002050!6.77e-10!605;UBERON:0005423!6.77e-10!605;UBERON:0001637!7.27e-10!42;UBERON:0003509!7.27e-10!42;UBERON:0004572!7.27e-10!42;UBERON:0001981!9.37e-10!60;UBERON:0007500!9.37e-10!60;UBERON:0004537!9.37e-10!60;UBERON:0006965!9.37e-10!60;UBERON:0002199!9.56e-10!45;UBERON:0002416!9.56e-10!45;UBERON:0002385!9.98e-10!63;UBERON:0001015!9.98e-10!63;UBERON:0000383!9.98e-10!63;UBERON:0002049!3.27e-09!79;UBERON:0007798!3.27e-09!79;UBERON:0002371!4.42e-09!80;UBERON:0000055!5.75e-09!69;UBERON:0005256!6.20e-09!143;UBERON:0002097!9.97e-09!40;UBERON:0000922!1.09e-08!612;UBERON:0004573!2.48e-08!33;UBERON:0004571!2.48e-08!33;UBERON:0002100!2.15e-07!216;UBERON:0003914!2.86e-07!118;UBERON:0004535!3.20e-07!110;UBERON:0001009!7.45e-07!113
|ontology_enrichment_uberon=UBERON:0002204!4.08e-23!167;UBERON:0000926!7.61e-20!448;UBERON:0004120!7.61e-20!448;UBERON:0006603!7.61e-20!448;UBERON:0003081!4.22e-16!216;UBERON:0000914!5.94e-15!83;UBERON:0002329!5.94e-15!83;UBERON:0003077!5.94e-15!83;UBERON:0003059!5.94e-15!83;UBERON:0007282!5.94e-15!83;UBERON:0009618!5.94e-15!83;UBERON:0007285!5.94e-15!83;UBERON:0000468!3.61e-14!659;UBERON:0000480!2.41e-13!626;UBERON:0004290!2.41e-13!70;UBERON:0000467!2.64e-13!625;UBERON:0000486!7.73e-13!82;UBERON:0004765!3.09e-12!101;UBERON:0001434!3.09e-12!101;UBERON:0002384!1.33e-10!375;UBERON:0003102!2.09e-10!95;UBERON:0001134!3.01e-10!61;UBERON:0002036!3.01e-10!61;UBERON:0003082!3.01e-10!61;UBERON:0001474!3.32e-10!86;UBERON:0004872!4.06e-10!84;UBERON:0000923!5.64e-10!604;UBERON:0005291!5.64e-10!604;UBERON:0006598!5.64e-10!604;UBERON:0002532!5.64e-10!604;UBERON:0002050!6.77e-10!605;UBERON:0005423!6.77e-10!605;UBERON:0001637!7.27e-10!42;UBERON:0003509!7.27e-10!42;UBERON:0004572!7.27e-10!42;UBERON:0001981!9.37e-10!60;UBERON:0007500!9.37e-10!60;UBERON:0004537!9.37e-10!60;UBERON:0006965!9.37e-10!60;UBERON:0002199!9.56e-10!45;UBERON:0002416!9.56e-10!45;UBERON:0002385!9.98e-10!63;UBERON:0001015!9.98e-10!63;UBERON:0000383!9.98e-10!63;UBERON:0002049!3.27e-09!79;UBERON:0007798!3.27e-09!79;UBERON:0002371!4.42e-09!80;UBERON:0000055!5.75e-09!69;UBERON:0005256!6.20e-09!143;UBERON:0002097!9.97e-09!40;UBERON:0000922!1.09e-08!612;UBERON:0004573!2.48e-08!33;UBERON:0004571!2.48e-08!33;UBERON:0002100!2.15e-07!216;UBERON:0003914!2.86e-07!118;UBERON:0004535!3.20e-07!110;UBERON:0001009!7.45e-07!113
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}}
}}

Revision as of 13:57, 5 September 2012


Full id: C4734_Fibroblast_Smooth_Mesenchymal_Preadipocyte_Keratocytes_Chondrocyte_melanoma



Phase1 CAGE Peaks

Hg19::chr8:145025046..145025061,-p7@PLEC
Hg19::chr8:145025063..145025073,-p16@PLEC
Hg19::chr8:145025074..145025102,-p2@PLEC


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 cell2.64e-33180
fibroblast6.82e-2875
somatic cell2.83e-26591
animal cell6.69e-23679
eukaryotic cell6.69e-23679
multi fate stem cell4.63e-16430
somatic stem cell5.95e-16436
mesodermal cell3.84e-15119
stem cell4.62e-14444
native cell9.74e-13722
skin fibroblast1.29e-1123
muscle precursor cell4.39e-1157
myoblast4.39e-1157
multi-potent skeletal muscle stem cell4.39e-1157
contractile cell4.60e-1159
CD14-positive, CD16-negative classical monocyte2.43e-1042
classical monocyte2.72e-1045
muscle cell3.94e-1054
connective tissue cell5.66e-10365
smooth muscle cell5.07e-0942
smooth muscle myoblast5.07e-0942
mesenchymal cell6.79e-09358
macrophage dendritic cell progenitor8.63e-0965
monopoietic cell1.31e-0863
monocyte1.31e-0863
monoblast1.31e-0863
promonocyte1.31e-0863
granulocyte monocyte progenitor cell6.78e-0871
preadipocyte1.70e-0712
electrically responsive cell2.07e-0760
electrically active cell2.07e-0760
embryonic cell2.40e-07248
motile cell4.56e-07390
myeloid lineage restricted progenitor cell4.65e-0770
Uber Anatomy
Ontology termp-valuen
musculoskeletal system4.08e-23167
mesoderm7.61e-20448
mesoderm-derived structure7.61e-20448
presumptive mesoderm7.61e-20448
lateral plate mesoderm4.22e-16216
somite5.94e-1583
paraxial mesoderm5.94e-1583
presomitic mesoderm5.94e-1583
presumptive segmental plate5.94e-1583
trunk paraxial mesoderm5.94e-1583
presumptive paraxial mesoderm5.94e-1583
multi-cellular organism3.61e-14659
anatomical group2.41e-13626
dermomyotome2.41e-1370
anatomical system2.64e-13625
multilaminar epithelium7.73e-1382
skeletal element3.09e-12101
skeletal system3.09e-12101
connective tissue1.33e-10375
surface structure2.09e-1095
skeletal muscle tissue3.01e-1061
striated muscle tissue3.01e-1061
myotome3.01e-1061
bone element3.32e-1086
splanchnic layer of lateral plate mesoderm4.06e-1084
germ layer5.64e-10604
embryonic tissue5.64e-10604
presumptive structure5.64e-10604
epiblast (generic)5.64e-10604
embryonic structure6.77e-10605
developing anatomical structure6.77e-10605
artery7.27e-1042
arterial blood vessel7.27e-1042
arterial system7.27e-1042
blood vessel9.37e-1060
epithelial tube open at both ends9.37e-1060
blood vasculature9.37e-1060
vascular cord9.37e-1060
integument9.56e-1045
integumental system9.56e-1045
muscle tissue9.98e-1063
musculature9.98e-1063
musculature of body9.98e-1063
vasculature3.27e-0979
vascular system3.27e-0979
bone marrow4.42e-0980
vessel5.75e-0969
trunk mesenchyme6.20e-09143
skin of body9.97e-0940
embryo1.09e-08612
systemic artery2.48e-0833
systemic arterial system2.48e-0833
trunk2.15e-07216
epithelial tube2.86e-07118
cardiovascular system3.20e-07110
circulatory system7.45e-07113


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
CCNT2#90536.336201576962630.003930750035764890.0191252552054623
E2F6#187635.017155731697390.00791769806886330.0324471833868556
EGR1#195834.988179094810140.008056488137383440.0322614763460063
ETS1#211339.728760922202340.001085840092584840.00765622828986415
FOS#235338.99795530889440.001372499272417130.00902262551217804
MXI1#460139.96157162875930.001011470541259020.00723689606484558
MYC#460935.22228187160940.007020843755740150.0296190782438902
ZBTB7A#5134137.35190930787590.002516255860282270.0140984573922757
ZNF263#1012738.221841637010680.001799043925565870.0110173770694367



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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