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Coexpression cluster:C579: Difference between revisions

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{{Coexpression_clusters
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filament bundle formation!0.00284618870874619!7429;10083$GO:0007015!actin filament organization!0.00680066143724809!7429;10083$GO:0004058!aromatic-L-amino-acid decarboxylase activity!0.0157482632756387!1644$GO:0030046!parallel actin filament bundle formation!0.0157482632756387!10083$GO:0001917!photoreceptor inner segment!0.0251938834677571!10083$GO:0051014!actin filament severing!0.0364213865634692!7429$GO:0007168!receptor guanylyl cyclase signaling pathway!0.0364213865634692!2984$GO:0032420!stereocilium!0.0364213865634692!10083$GO:0032421!stereocilium bundle!0.0364213865634692!10083$GO:0001750!photoreceptor outer segment!0.0364213865634692!10083$GO:0030036!actin cytoskeleton organization and biogenesis!0.0364213865634692!7429;10083$GO:0050957!equilibrioception!0.0364213865634692!10083$GO:0030029!actin filament-based process!0.0364213865634692!7429;10083$GO:0031513!nonmotile primary cilium!0.0364213865634692!10083$GO:0004383!guanylate cyclase activity!0.0364213865634692!2984$GO:0016829!lyase activity!0.0364213865634692!2984;1644$GO:0042423!catecholamine biosynthetic process!0.0364213865634692!1644$GO:0046068!cGMP metabolic process!0.0364213865634692!2984$GO:0006182!cGMP biosynthetic process!0.0364213865634692!2984$GO:0042491!auditory receptor cell differentiation!0.0369540344387369!10083$GO:0042995!cell projection!0.0369540344387369!2984;10083$GO:0042490!mechanoreceptor differentiation!0.0392977188640581!10083$GO:0060113!inner ear receptor cell differentiation!0.0392977188640581!10083$GO:0045494!photoreceptor cell maintenance!0.0392977188640581!10083$GO:0000086!G2/M transition of mitotic cell cycle!0.0401284692083886!10083$GO:0050885!neuromuscular process controlling balance!0.0401284692083886!10083$GO:0005902!microvillus!0.0401284692083886!10083$GO:0008290!F-actin capping protein complex!0.0401284692083886!7429$GO:0051693!actin filament capping!0.0401284692083886!7429$GO:0051016!barbed-end actin filament capping!0.0401284692083886!7429$GO:0030835!negative regulation of actin filament depolymerization!0.0401284692083886!7429$GO:0050905!neuromuscular process!0.0401284692083886!10083$GO:0005903!brush border!0.0401284692083886!2984$GO:0030834!regulation of actin filament depolymerization!0.0401284692083886!7429$GO:0030042!actin filament depolymerization!0.0401284692083886!7429$GO:0046847!filopodium formation!0.0401284692083886!80115$GO:0030035!microspike biogenesis!0.0407360836108583!80115$GO:0006584!catecholamine metabolic process!0.0423741530874236!1644$GO:0018958!phenol metabolic process!0.0423741530874236!1644$GO:0042472!inner ear morphogenesis!0.0423741530874236!10083$GO:0042471!ear morphogenesis!0.0474400479121247!10083$GO:0009975!cyclase activity!0.0481390800315232!2984$GO:0016849!phosphorus-oxygen lyase activity!0.0481390800315232!2984$GO:0042401!biogenic amine biosynthetic 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;0.0966405,MA0102.2;1.1957,MA0258.1;0.964206,MA0259.1;0.104286,MA0442.1;0}}
|full_id=C579_small_argyrophil_colon_duodenum_signet_temporal_Intestinal
|id=C579
}}

Latest revision as of 11:26, 17 September 2013


Full id: C579_small_argyrophil_colon_duodenum_signet_temporal_Intestinal



Phase1 CAGE Peaks

Hg19::chr10:129691195..129691212,-p1@CLRN3
Hg19::chr11:17565907..17565933,-p1@USH1C
Hg19::chr11:17565934..17565939,-p8@USH1C
Hg19::chr11:17565951..17565982,-p2@USH1C
Hg19::chr12:14849553..14849558,-p5@GUCY2C
Hg19::chr12:14849578..14849586,-p3@GUCY2C
Hg19::chr14:39703084..39703110,+p10@CTAGE5
Hg19::chr16:21244993..21245042,+p1@ANKS4B
Hg19::chr17:55163280..55163297,+p14@AKAP1
Hg19::chr22:38506619..38506678,-p2@BAIAP2L2
Hg19::chr2:219283836..219283853,+p1@VIL1
Hg19::chr2:219290413..219290430,+p@chr2:219290413..219290430
+
Hg19::chr4:40477740..40477760,-p19@RBM47
Hg19::chr4:40477770..40477783,-p23@RBM47
Hg19::chr7:50633078..50633140,-p1@DDC


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:0051017actin filament bundle formation0.00284618870874619
GO:0007015actin filament organization0.00680066143724809
GO:0004058aromatic-L-amino-acid decarboxylase activity0.0157482632756387
GO:0030046parallel actin filament bundle formation0.0157482632756387
GO:0001917photoreceptor inner segment0.0251938834677571
GO:0051014actin filament severing0.0364213865634692
GO:0007168receptor guanylyl cyclase signaling pathway0.0364213865634692
GO:0032420stereocilium0.0364213865634692
GO:0032421stereocilium bundle0.0364213865634692
GO:0001750photoreceptor outer segment0.0364213865634692
GO:0030036actin cytoskeleton organization and biogenesis0.0364213865634692
GO:0050957equilibrioception0.0364213865634692
GO:0030029actin filament-based process0.0364213865634692
GO:0031513nonmotile primary cilium0.0364213865634692
GO:0004383guanylate cyclase activity0.0364213865634692
GO:0016829lyase activity0.0364213865634692
GO:0042423catecholamine biosynthetic process0.0364213865634692
GO:0046068cGMP metabolic process0.0364213865634692
GO:0006182cGMP biosynthetic process0.0364213865634692
GO:0042491auditory receptor cell differentiation0.0369540344387369
GO:0042995cell projection0.0369540344387369
GO:0042490mechanoreceptor differentiation0.0392977188640581
GO:0060113inner ear receptor cell differentiation0.0392977188640581
GO:0045494photoreceptor cell maintenance0.0392977188640581
GO:0000086G2/M transition of mitotic cell cycle0.0401284692083886
GO:0050885neuromuscular process controlling balance0.0401284692083886
GO:0005902microvillus0.0401284692083886
GO:0008290F-actin capping protein complex0.0401284692083886
GO:0051693actin filament capping0.0401284692083886
GO:0051016barbed-end actin filament capping0.0401284692083886
GO:0030835negative regulation of actin filament depolymerization0.0401284692083886
GO:0050905neuromuscular process0.0401284692083886
GO:0005903brush border0.0401284692083886
GO:0030834regulation of actin filament depolymerization0.0401284692083886
GO:0030042actin filament depolymerization0.0401284692083886
GO:0046847filopodium formation0.0401284692083886
GO:0030035microspike biogenesis0.0407360836108583
GO:0006584catecholamine metabolic process0.0423741530874236
GO:0018958phenol metabolic process0.0423741530874236
GO:0042472inner ear morphogenesis0.0423741530874236
GO:0042471ear morphogenesis0.0474400479121247
GO:0009975cyclase activity0.0481390800315232
GO:0016849phosphorus-oxygen lyase activity0.0481390800315232
GO:0042401biogenic amine biosynthetic process0.0484642007416722



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
metabolising cell1.81e-1012
endopolyploid cell1.81e-1012
parenchymal cell1.81e-1012
polyploid cell1.81e-1012
hepatocyte1.81e-1012
endodermal cell1.94e-0858
epithelial cell of stomach1.86e-073
Uber Anatomy
Ontology termp-valuen
gastrointestinal system7.79e-3625
intestine4.97e-3317
large intestine4.64e-2211
subdivision of digestive tract3.57e-19118
lower digestive tract2.18e-165
digestive system3.74e-16145
digestive tract3.74e-16145
primitive gut3.74e-16145
colon3.11e-149
endoderm-derived structure3.92e-14160
endoderm3.92e-14160
presumptive endoderm3.92e-14160
digestive tract diverticulum1.09e-1223
rectum4.49e-124
epithelium of foregut-midgut junction1.22e-1125
anatomical boundary1.22e-1125
hepatobiliary system1.22e-1125
foregut-midgut junction1.22e-1125
septum transversum1.22e-1125
sac4.39e-1126
small intestine2.45e-104
hepatic diverticulum2.78e-1022
liver primordium2.78e-1022
gut epithelium3.17e-0954
abdomen element3.70e-0954
abdominal segment element3.70e-0954
liver4.82e-0919
digestive gland4.82e-0919
liver bud4.82e-0919
epithelial sac6.12e-0925
organ system subdivision1.84e-08223
abdominal segment of trunk4.89e-0860
abdomen4.89e-0860
multi-tissue structure6.61e-07342
trunk region element9.69e-07101
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma6.13e-112
gastrointestinal system cancer1.03e-0814
adenocarcinoma9.83e-0725


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)
MA0003.10.0132214
MA0004.10.256222
MA0006.10.137644
MA0007.10.67744
MA0009.10.669377
MA0014.10.533948
MA0017.12.911
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.12.67755
MA0048.10.441458
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.0154739
MA0056.10
MA0057.10.420982
MA0058.10.182945
MA0059.10.182001
MA0060.10.51173
MA0061.10.198509
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.616525
MA0069.10.655419
MA0070.10.644843
MA0071.10.831024
MA0072.10.640598
MA0073.18.00756e-06
MA0074.10.337035
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.11.62113
MA0084.11.15904
MA0087.10.63829
MA0088.10.426561
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.647316
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.141917
MA0103.10.411001
MA0105.10.376193
MA0106.10.37688
MA0107.10.0950422
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.12.15005
MA0115.14.91533
MA0116.11.09759
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.0838502
MA0145.11.04117
MA0146.10.454099
MA0147.10.326612
MA0148.10.276339
MA0149.10.298252
MA0062.20.0512998
MA0035.20.824687
MA0039.21.29697
MA0138.20.425279
MA0002.20.0612545
MA0137.20.153033
MA0104.20.236755
MA0047.20.366327
MA0112.20.448515
MA0065.20.751536
MA0150.11.10274
MA0151.10
MA0152.10.311809
MA0153.13.00863
MA0154.10.187751
MA0155.10.0403226
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.327637
MA0160.11.43316
MA0161.10
MA0162.10.13181
MA0163.10.0128736
MA0164.11.03839
MA0080.20.432036
MA0018.20.378086
MA0099.20.312108
MA0079.20.0966405
MA0102.21.1957
MA0258.10.964206
MA0259.10.104286
MA0442.10



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
HDAC2#306654.471873412208750.003658657523086560.0184762116461311
HNF4A#317269.252916145181482.32447243124585e-050.000507241070302727
HNF4G#317447.667579340385810.001465855192095080.00938987060888236



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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