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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1158_Small_malignant_Gingival_Keratinocyte_cervical_Mallassezderived_oral
|full_id=C1158_Small_malignant_Gingival_Keratinocyte_cervical_Mallassezderived_oral
|gostat_on_coexpression_clusters=GO:0005923!tight junction!0.0123631225715295!154810$GO:0043296!apical junction complex!0.0123631225715295!154810$GO:0016327!apicolateral plasma membrane!0.0123631225715295!154810$GO:0005911!intercellular junction!0.0152772871776757!154810$GO:0042802!identical protein binding!0.0252560932532674!154810$GO:0030054!cell junction!0.0252560932532674!154810
|gostat_on_coexpression_clusters=GO:0005923!tight junction!0.0123631225715295!154810$GO:0043296!apical junction complex!0.0123631225715295!154810$GO:0016327!apicolateral plasma membrane!0.0123631225715295!154810$GO:0005911!intercellular junction!0.0152772871776757!154810$GO:0042802!identical protein binding!0.0252560932532674!154810$GO:0030054!cell junction!0.0252560932532674!154810

Revision as of 13:38, 12 September 2012


Full id: C1158_Small_malignant_Gingival_Keratinocyte_cervical_Mallassezderived_oral



Phase1 CAGE Peaks

Hg19::chr11:94439579..94439590,+p11@AMOTL1
Hg19::chr11:94439591..94439602,+p7@AMOTL1
Hg19::chr11:94439606..94439641,+p2@AMOTL1
Hg19::chr11:94439650..94439668,+p4@AMOTL1
Hg19::chr11:94439679..94439690,+p9@AMOTL1
Hg19::chr14:81790540..81790556,-p@chr14:81790540..81790556
-
Hg19::chr1:209605563..209605577,+p1@MIR205
p2@MIR205HG


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

GO IDGO nameFDR corrected p-value
GO:0005923tight junction0.0123631225715295
GO:0043296apical junction complex0.0123631225715295
GO:0016327apicolateral plasma membrane0.0123631225715295
GO:0005911intercellular junction0.0152772871776757
GO:0042802identical protein binding0.0252560932532674
GO:0030054cell junction0.0252560932532674



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 cell1.79e-18254
endo-epithelial cell2.61e-1743
endodermal cell1.51e-1159
epithelial cell of alimentary canal4.39e-1021
respiratory epithelial cell5.37e-0813
general ecto-epithelial cell3.76e-0713
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure7.29e-17169
ectoderm4.34e-16173
presumptive ectoderm4.34e-16173
anterior region of body7.03e-16129
craniocervical region7.03e-16129
adult organism1.12e-15115
head6.81e-15123
respiratory system9.93e-1472
organ part2.93e-13219
organ9.03e-12511
endoderm-derived structure2.28e-11169
endoderm2.28e-11169
presumptive endoderm2.28e-11169
embryo4.59e-11612
anatomical group7.74e-11626
anatomical system9.48e-11625
multi-cellular organism1.64e-10659
multi-tissue structure5.19e-10347
regional part of nervous system1.51e-0994
nervous system1.51e-0994
neural plate1.70e-0986
presumptive neural plate1.70e-0986
embryonic structure2.40e-09605
developing anatomical structure2.40e-09605
central nervous system2.46e-0982
pre-chordal neural plate3.49e-0961
respiratory tract4.56e-0953
germ layer4.71e-09604
embryonic tissue4.71e-09604
presumptive structure4.71e-09604
epiblast (generic)4.71e-09604
organism subdivision7.17e-09365
neurectoderm1.05e-0890
neural tube1.61e-0857
neural rod1.61e-0857
future spinal cord1.61e-0857
neural keel1.61e-0857
digestive system4.48e-08155
digestive tract4.48e-08155
primitive gut4.48e-08155
brain4.51e-0869
future brain4.51e-0869
anterior neural tube5.54e-0842
orifice5.95e-0835
regional part of forebrain1.18e-0741
forebrain1.18e-0741
future forebrain1.18e-0741
oral opening1.56e-0721
mixed endoderm/mesoderm-derived structure2.01e-07130
regional part of brain3.53e-0759
internal genitalia3.64e-0725
subdivision of digestive tract4.46e-07129
endodermal part of digestive tract4.46e-07129
gray matter5.92e-0734
brain grey matter5.92e-0734
telencephalon9.42e-0734
Disease
Ontology termp-valuen
carcinoma1.69e-10106
squamous cell carcinoma2.15e-1014


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
POLR2A#543072.147453176558070.004747636447610280.0223300339091182
STAT3#677457.513903569395890.0001381820449413220.0018050774973892
TRIM28#10155513.27894646090188.62103642667186e-060.000234045340100125



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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