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Coexpression cluster:C3821: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190048425066085!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279444126869868!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915091023515678!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462294227514793!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00581209620833851!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154107260223909!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294501526630953!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00543029389921847!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242761538983957
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190048425066085!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279444126869868!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915091023515678!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462294227514793!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00581209620833851!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154107260223909!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294501526630953!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00543029389921847!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242761538983957
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}}
}}

Revision as of 16:22, 26 November 2012


Full id: C3821_lung_seminal_small_salivary_parotid_ductus_colon



Phase1 CAGE Peaks

Hg19::chr19:54676833..54676838,-p3@TMC4
Hg19::chr19:54676846..54676872,-p1@TMC4
Hg19::chr19:54676884..54676893,-p2@TMC4


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
endoderm-derived structure3.32e-25160
endoderm3.32e-25160
presumptive endoderm3.32e-25160
digestive system2.46e-20145
digestive tract2.46e-20145
primitive gut2.46e-20145
subdivision of digestive tract2.47e-17118
respiratory system1.49e-1474
anatomical space4.68e-1395
endo-epithelium4.95e-1382
immaterial anatomical entity1.97e-11117
epithelial bud2.73e-1137
trunk region element4.36e-11101
thoracic cavity element6.43e-1134
thoracic cavity6.43e-1134
respiratory tract6.98e-1154
thoracic segment organ2.02e-1035
foregut1.51e-0987
epithelial fold1.87e-0947
thoracic segment of trunk2.73e-0952
organism subdivision5.17e-09264
subdivision of trunk5.46e-09112
urinary system structure1.38e-0847
intestine2.44e-0817
orifice2.83e-0836
renal system2.89e-0848
lung3.22e-0822
respiratory tube3.22e-0822
respiration organ3.22e-0822
pair of lungs3.22e-0822
lung primordium3.22e-0822
lung bud3.22e-0822
gastrointestinal system1.24e-0725
reproductive structure1.31e-0759
reproductive system1.31e-0759
respiratory primordium3.05e-0738
endoderm of foregut3.05e-0738
organ3.36e-07503
respiratory system epithelium3.89e-0728
urothelium4.40e-075
male organism5.67e-0722
male reproductive system5.67e-0722
male reproductive organ8.68e-0711
Disease
Ontology termp-valuen
carcinoma1.26e-18106
cell type cancer7.77e-13143
squamous cell carcinoma2.51e-1214
adenocarcinoma5.95e-1225


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)

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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#90536.336201576962630.003930750035764890.0190048425066085
CTCF#1066435.360256373075030.0064925092527670.0279444126869868
EBF1#187938.9064668465690.00141523283560980.00915091023515678
ELF1#199734.258097958807540.01295179875054610.0462294227514793
FOXA1#3169311.08141974938550.000734755275698670.00581209620833851
GABPB1#255337.067683836182170.002832212825417420.0154107260223909
MYC#460935.22228187160940.007020843755740150.0294501526630953
TAF7#6879311.43306940492390.0006690181981945830.00543029389921847
ZEB1#6935316.88843201754390.0002075486917327580.00242761538983957



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.