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Coexpression cluster:C3405: Difference between revisions

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|tf_chipseq_enrich=GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387239025006005
|tf_chipseq_enrich=GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387239025006005
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}}
}}

Revision as of 16:07, 26 November 2012


Full id: C3405_squamous_Urothelial_Mallassezderived_Sebocyte_Gingival_Small_Prostate



Phase1 CAGE Peaks

Hg19::chr14:21510433..21510440,+p4@RNASE7
Hg19::chr14:21510460..21510479,+p2@RNASE7
Hg19::chr14:21510487..21510506,+p3@RNASE7


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
endo-epithelial cell2.70e-3542
endodermal cell1.04e-2558
epithelial cell1.03e-20253
epithelial cell of alimentary canal1.67e-2020
respiratory epithelial cell3.68e-2013
general ecto-epithelial cell3.50e-1914
acinar cell3.05e-145
transitional epithelial cell9.14e-134
urothelial cell9.14e-134
protein secreting cell8.38e-126
squamous epithelial cell3.53e-1163
epithelial cell of tracheobronchial tree2.52e-109
epithelial cell of lower respiratory tract2.52e-109
gingival epithelial cell6.14e-103
epithelial cell of Malassez1.03e-093
ecto-epithelial cell1.14e-0934
duct epithelial cell7.33e-093
branched duct epithelial cell7.33e-093
tracheal epithelial cell7.33e-093
tracheoblast7.33e-093
acinar cell of salivary gland1.02e-083
bronchial epithelial cell1.13e-083
chorionic membrane mesenchymal stem cell1.26e-083
epidermal cell3.96e-089
stratified squamous epithelial cell6.56e-086
keratin accumulating cell6.56e-086
stratified epithelial cell6.56e-086
keratinizing barrier epithelial cell6.56e-086
epithelial fate stem cell6.56e-086
stratified epithelial stem cell6.56e-086
surface ectodermal cell6.56e-086
glandular epithelial cell9.90e-089
mammary gland epithelial cell2.00e-074
sebum secreting cell3.20e-072
epithelial cell of sweat gland3.20e-072
epithelial cell of skin gland3.20e-072
acinar cell of sebaceous gland3.20e-072
embryonic cell4.96e-07250
Uber Anatomy
Ontology termp-valuen
respiratory system8.71e-2074
oral opening3.72e-1822
orifice8.44e-1836
endoderm-derived structure6.03e-17160
endoderm6.03e-17160
presumptive endoderm6.03e-17160
surface structure5.55e-1699
urothelium2.94e-155
mouth2.96e-1529
stomodeum2.96e-1529
mucosa1.17e-1420
anterior region of body5.22e-1462
craniocervical region5.22e-1462
head5.29e-1356
mouth mucosa8.67e-1313
transitional epithelium1.22e-126
respiratory tract8.81e-1254
mucosa of oral region4.11e-114
respiratory system mucosa4.11e-114
pharynx1.48e-1011
subdivision of head2.22e-1049
gingival epithelium6.14e-103
digestive system1.40e-09145
digestive tract1.40e-09145
primitive gut1.40e-09145
neck7.06e-0910
chordate pharynx9.66e-0910
pharyngeal region of foregut9.66e-0910
lower respiratory tract epithelium1.13e-083
epithelium of bronchus1.13e-083
tongue1.19e-083
gustatory system1.19e-083
future tongue1.19e-083
acellular anatomical structure1.26e-083
egg chorion1.26e-083
pharyngeal arch system1.97e-0818
respiratory system epithelium9.10e-0828
segment of respiratory tract9.84e-0847
mammary gland2.00e-074
mammary bud2.00e-074
mammary ridge2.00e-074
mammary placode2.00e-074
jaw skeleton2.32e-074
splanchnocranium2.32e-074
skin gland3.20e-072
epidermis gland3.20e-072
gland of integumental system3.20e-072
sebaceous gland3.20e-072
skin sebaceous gland3.20e-072
sweat gland3.20e-072
sweat gland placode3.20e-072
sebaceous gland placode3.20e-072
subdivision of digestive tract9.73e-07118
organ component layer9.97e-0766
Disease
Ontology termp-valuen
squamous cell carcinoma1.18e-2114


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
GATA1#2623313.56030814380040.0004009615963782630.00387239025006005



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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