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Coexpression cluster:C4353: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4353_heart_penis_aorta_smooth_sacrococcigeal_Mast_mesodermal
|full_id=C4353_heart_penis_aorta_smooth_sacrococcigeal_Mast_mesodermal
|id=C4353
|id=C4353

Revision as of 17:25, 12 September 2012


Full id: C4353_heart_penis_aorta_smooth_sacrococcigeal_Mast_mesodermal



Phase1 CAGE Peaks

Hg19::chr3:99594980..99594993,-p3@FILIP1L
Hg19::chr3:99594998..99595024,-p1@FILIP1L
Hg19::chr3:99595037..99595051,-p2@FILIP1L


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
mesodermal cell1.12e-09119
muscle precursor cell6.13e-0757
myoblast6.13e-0757
multi-potent skeletal muscle stem cell6.13e-0757
non-terminally differentiated cell7.13e-07180
fibroblast7.67e-0775
Uber Anatomy
Ontology termp-valuen
multi-cellular organism4.35e-16659
anatomical system3.99e-14625
anatomical group5.05e-14626
trunk mesenchyme2.87e-13143
epithelium3.36e-11309
organism subdivision4.76e-11365
cell layer5.03e-11312
unilaminar epithelium2.75e-10138
epithelial tube4.03e-10118
anatomical conduit8.21e-10241
trunk8.49e-10216
somite1.92e-0983
paraxial mesoderm1.92e-0983
presomitic mesoderm1.92e-0983
presumptive segmental plate1.92e-0983
trunk paraxial mesoderm1.92e-0983
presumptive paraxial mesoderm1.92e-0983
multilaminar epithelium2.89e-0982
muscle tissue5.79e-0963
musculature5.79e-0963
musculature of body5.79e-0963
splanchnic layer of lateral plate mesoderm8.06e-0984
multi-tissue structure1.18e-08347
vasculature1.86e-0879
vascular system1.86e-0879
anatomical cluster2.37e-08286
dermomyotome2.75e-0870
skeletal muscle tissue3.54e-0861
striated muscle tissue3.54e-0861
myotome3.54e-0861
organ4.57e-08511
embryonic structure6.42e-08605
developing anatomical structure6.42e-08605
germ layer1.25e-07604
embryonic tissue1.25e-07604
presumptive structure1.25e-07604
epiblast (generic)1.25e-07604
vessel1.50e-0769
embryo1.92e-07612
mesoderm7.33e-07448
mesoderm-derived structure7.33e-07448
presumptive mesoderm7.33e-07448


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#90536.336201576962630.003930750035764890.0190692866492591
CEBPB#105137.971147625824820.001974187055288560.0115559983111356
CTCF#1066435.360256373075030.0064925092527670.0280600527146589
E2F1#186934.907389214879320.008460985347239390.0326784086638931
E2F6#187635.017155731697390.00791769806886330.0323583043871655
EGR1#195834.988179094810140.008056488137383440.0321775809621855
ELF1#199734.258097958807540.01295179875054610.0464006898225948
FOXA1#3169311.08141974938550.000734755275698670.00582975812798703
JUN#3725312.51282919233630.0005103313992726250.00445490647012986
JUND#372736.994663941871030.002921845042734990.015727995795186
NFKB1#479035.488063424193840.006049381815655430.0270377621194521
POU5F1#54603335.4392014519062.63510205045339e-081.82256571554505e-06
RAD21#5885310.35503389545630.0009004912073565420.00666664784894803
SRF#6722313.79717826216780.0003806615025800190.00375871293069439
ZBTB7A#5134137.35190930787590.002516255860282270.0140645033873171
ZEB1#6935316.88843201754390.0002075486917327580.00243333832688342



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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