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Coexpression cluster:C4255: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4255_Adipocyte_amniotic_Smooth_Chondrocyte_chorionic_Ewing_Preadipocyte
|full_id=C4255_Adipocyte_amniotic_Smooth_Chondrocyte_chorionic_Ewing_Preadipocyte
|id=C4255
|id=C4255

Revision as of 17:18, 12 September 2012


Full id: C4255_Adipocyte_amniotic_Smooth_Chondrocyte_chorionic_Ewing_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr3:100211412..100211501,+p1@TMEM45A
Hg19::chr3:100211526..100211584,+p2@TMEM45A
Hg19::chr3:100211600..100211628,+p4@TMEM45A


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
somite1.78e-1683
paraxial mesoderm1.78e-1683
presomitic mesoderm1.78e-1683
presumptive segmental plate1.78e-1683
trunk paraxial mesoderm1.78e-1683
presumptive paraxial mesoderm1.78e-1683
trunk mesenchyme1.46e-15143
multilaminar epithelium1.65e-1582
dermomyotome5.70e-1570
trunk3.38e-14216
skeletal muscle tissue1.31e-1361
striated muscle tissue1.31e-1361
myotome1.31e-1361
mesenchyme3.47e-13238
entire embryonic mesenchyme3.47e-13238
muscle tissue3.89e-1363
musculature3.89e-1363
musculature of body3.89e-1363
multi-cellular organism7.97e-13659
organism subdivision8.64e-13365
multi-tissue structure4.02e-11347
splanchnic layer of lateral plate mesoderm2.57e-1084
surface structure1.63e-0995
unilaminar epithelium2.51e-09138
anatomical group7.43e-09626
anatomical system9.06e-09625
artery1.98e-0842
arterial blood vessel1.98e-0842
arterial system1.98e-0842
extraembryonic membrane3.07e-0814
membranous layer3.07e-0814
integument3.27e-0845
integumental system3.27e-0845
systemic artery3.37e-0833
systemic arterial system3.37e-0833
organ component layer3.99e-0857
epithelial tube5.96e-08118
extraembryonic structure1.83e-0724
anatomical cluster2.65e-07286
cell layer6.70e-07312
embryo6.80e-07612
skin of body6.86e-0740
primordium7.45e-07168
Disease
Ontology termp-valuen
ovarian cancer1.72e-0714


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#90536.336201576962630.003930750035764890.0190560090509794
CHD2#1106310.34402283411690.0009033701102746880.00661759633492166
CTCF#1066435.360256373075030.0064925092527670.0280333708388347
E2F1#186934.907389214879320.008460985347239390.0326434003945451
E2F6#187635.017155731697390.00791769806886330.0323279435714459
EBF1#187938.9064668465690.00141523283560980.0091736284830097
ELF1#199734.258097958807540.01295179875054610.0463656992427601
FOS#235338.99795530889440.001372499272417130.00899657638310253
GABPB1#255337.067683836182170.002832212825417420.0154509755157632
IRF1#365937.63716375356390.002244692747297240.0128421509632965
IRF3#3661346.98195221148969.63568551583244e-060.000253870171439966
NFYA#4800318.42558069983050.0001598135507814160.00200057142874989
NFYB#4801316.75979325353650.0002123649923296180.00246353298166311
NRF1#4899312.21027944771090.0005492172401020010.00472251764688069
PAX5#507936.669565531177830.003370290999677260.0173308627137023
PBX3#5090321.91451268674419.49854535978121e-050.00137019140722402
RAD21#5885310.35503389545630.0009004912073565420.00666003832625946
RFX5#5993312.04791082719510.0005717246050312580.00485647385318093
SP1#666735.69838137814090.005403962701712170.0247179284633696
SP2#6668326.15353049384465.58768218891694e-050.000941700726364847
SPI1#668838.204323508522730.001810593189410520.0109247525627619
TCF12#6938310.63446490218640.0008313523990202070.00630450284644724
TCF7L2#6934310.77017656313730.0008003181298398380.00615632504694283
TFAP2A#7020316.5186343730450.0002218033880766340.00248844387660711
TFAP2C#7022310.80922860986020.0007916746575753130.00617258003452841



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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