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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C393_amniotic_Placental_Amniotic_clear_Basophils_pharyngeal_tonsil
|full_id=C393_amniotic_Placental_Amniotic_clear_Basophils_pharyngeal_tonsil
|gostat_on_coexpression_clusters=GO:0005595!collagen type XII!0.0282266369397579!1303$GO:0030020!extracellular matrix structural constituent conferring tensile strength!0.0282266369397579!1303$GO:0005861!troponin complex!0.0344718141264407!7140$GO:0005593!FACIT collagen!0.0344718141264407!1303$GO:0006942!regulation of striated muscle contraction!0.0344718141264407!7140$GO:0030934!anchoring collagen!0.0344718141264407!1303$GO:0005515!protein binding!0.0344718141264407!6274;1607;144568;7140;8581;1303$GO:0030199!collagen fibril organization!0.0344718141264407!1303$GO:0005865!striated muscle thin filament!0.0344718141264407!7140
|gostat_on_coexpression_clusters=GO:0005595!collagen type XII!0.0282266369397579!1303$GO:0030020!extracellular matrix structural constituent conferring tensile strength!0.0282266369397579!1303$GO:0005861!troponin complex!0.0344718141264407!7140$GO:0005593!FACIT collagen!0.0344718141264407!1303$GO:0006942!regulation of striated muscle contraction!0.0344718141264407!7140$GO:0030934!anchoring collagen!0.0344718141264407!1303$GO:0005515!protein binding!0.0344718141264407!6274;1607;144568;7140;8581;1303$GO:0030199!collagen fibril organization!0.0344718141264407!1303$GO:0005865!striated muscle thin filament!0.0344718141264407!7140

Revision as of 16:56, 12 September 2012


Full id: C393_amniotic_Placental_Amniotic_clear_Basophils_pharyngeal_tonsil



Phase1 CAGE Peaks

Hg19::chr11:1946152..1946161,+p12@TNNT3
Hg19::chr12:83148856..83148864,+p@chr12:83148856..83148864
+
Hg19::chr12:8975061..8975072,+p5@A2ML1
Hg19::chr13:30415684..30415696,-p@chr13:30415684..30415696
-
Hg19::chr16:70740254..70740259,-p@chr16:70740254..70740259
-
Hg19::chr1:153520959..153520976,-p6@S100A3
Hg19::chr21:39670082..39670093,+p@chr21:39670082..39670093
+
Hg19::chr21:39670125..39670140,+p@chr21:39670125..39670140
+
Hg19::chr3:134044856..134044890,+p@chr3:134044856..134044890
+
Hg19::chr3:146323019..146323049,-p1@PLSCR5
Hg19::chr3:24339226..24339231,-p@chr3:24339226..24339231
-
Hg19::chr3:54925405..54925424,+p@chr3:54925405..54925424
+
Hg19::chr3:54925431..54925442,+p@chr3:54925431..54925442
+
Hg19::chr3:55513517..55513530,-p@chr3:55513517..55513530
-
Hg19::chr4:38062660..38062664,+p@chr4:38062660..38062664
+
Hg19::chr5:170210042..170210086,-p@chr5:170210042..170210086
-
Hg19::chr5:170210721..170210734,+p1@GABRP
Hg19::chr5:170238215..170238225,+p@chr5:170238215..170238225
+
Hg19::chr5:170239966..170239982,+p@chr5:170239966..170239982
+
Hg19::chr5:170241044..170241049,-p@chr5:170241044..170241049
-
Hg19::chr6:75828835..75828850,-p21@COL12A1
Hg19::chr6:75828851..75828864,-p20@COL12A1
Hg19::chr6:75828867..75828885,-p10@COL12A1
Hg19::chr7:114542043..114542046,-p@chr7:114542043..114542046
-
Hg19::chr7:14880892..14880938,-p16@DGKB
Hg19::chr8:143867355..143867390,-p2@LY6D
Hg19::chr8:8318890..8318903,-p1@ENST00000521218


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:0005595collagen type XII0.0282266369397579
GO:0030020extracellular matrix structural constituent conferring tensile strength0.0282266369397579
GO:0005861troponin complex0.0344718141264407
GO:0005593FACIT collagen0.0344718141264407
GO:0006942regulation of striated muscle contraction0.0344718141264407
GO:0030934anchoring collagen0.0344718141264407
GO:0005515protein binding0.0344718141264407
GO:0030199collagen fibril organization0.0344718141264407
GO:0005865striated muscle thin filament0.0344718141264407



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 cell5.28e-0843
epithelial cell4.22e-07254
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.21e-15169
endoderm4.21e-15169
presumptive endoderm4.21e-15169
digestive system4.11e-13155
digestive tract4.11e-13155
primitive gut4.11e-13155
organ component layer1.37e-1157
mixed endoderm/mesoderm-derived structure1.72e-11130
surface structure2.64e-1195
extraembryonic membrane1.71e-1014
membranous layer1.71e-1014
respiratory system6.57e-1072
subdivision of digestive tract6.42e-09129
endodermal part of digestive tract6.42e-09129
organ4.79e-08511
mouth1.41e-0728
stomodeum1.41e-0728
orifice2.64e-0735
extraembryonic structure6.92e-0724
multi-cellular organism7.37e-07659
Disease
Ontology termp-valuen
carcinoma8.42e-10106


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


No analysis results for this cluster

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.