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Coexpression cluster:C3821

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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>


Cell Type
Ontology termp-valuen
epithelial cell3.05e-24254
endo-epithelial cell2.61e-1943
endodermal cell1.98e-1459
respiratory epithelial cell1.54e-0913
epithelial cell of alimentary canal6.62e-0921
general ecto-epithelial cell2.14e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.57e-26169
endoderm4.57e-26169
presumptive endoderm4.57e-26169
digestive system1.81e-20155
digestive tract1.81e-20155
primitive gut1.81e-20155
subdivision of digestive tract2.88e-18129
endodermal part of digestive tract2.88e-18129
anatomical space2.58e-17104
immaterial anatomical entity8.02e-16126
mixed endoderm/mesoderm-derived structure1.27e-15130
respiratory system2.31e-1472
endo-epithelium3.12e-1282
trunk region element3.33e-11107
epithelial bud4.71e-1137
thoracic cavity element1.05e-1034
thoracic cavity1.05e-1034
foregut1.64e-1098
thoracic segment organ3.52e-1035
respiratory tract4.69e-1053
renal system4.89e-1045
orifice7.78e-1035
urinary system structure1.16e-0944
organ1.57e-09511
epithelial fold1.76e-0951
subdivision of trunk4.86e-09113
intermediate mesoderm1.64e-0837
anatomical cavity2.15e-0870
reproductive structure2.23e-0859
reproductive system2.23e-0859
thoracic segment of trunk2.43e-0852
lung7.36e-0822
respiratory tube7.36e-0822
respiration organ7.36e-0822
pair of lungs7.36e-0822
lung primordium7.36e-0822
lung bud7.36e-0822
multi-cellular organism9.92e-08659
gland1.12e-0759
duct1.13e-0726
oral opening1.71e-0721
male organism2.37e-0722
male reproductive system2.37e-0722
embryo2.76e-07612
reproductive organ3.92e-0748
male reproductive organ5.99e-0711
multi-tissue structure6.25e-07347
respiratory primordium6.49e-0738
endoderm of foregut6.49e-0738
adult organism6.67e-07115
mesenchyme7.37e-07238
entire embryonic mesenchyme7.37e-07238
gastrointestinal system7.96e-0735
tracheobronchial tree9.55e-0714
lower respiratory tract9.55e-0714
Disease
Ontology termp-valuen
carcinoma7.16e-18106
cell type cancer2.46e-11143
squamous cell carcinoma1.31e-1014
adenocarcinoma5.41e-1025


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#90536.336201576962630.003930750035764890.0190048425066085
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.