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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:39, 17 September 2013


Full id: C1157_Hepatic_neuroectodermal_liver_Hepatocyte_Adipocyte_spleen_kidney



Phase1 CAGE Peaks

Hg19::chr11:940729..940745,+p5@AP2A2
Hg19::chr19:7861495..7861500,+p@chr19:7861495..7861500
+
Hg19::chr3:58196639..58196653,-p2@DNASE1L3
Hg19::chr3:58196655..58196668,-p3@DNASE1L3
Hg19::chr3:58196822..58196832,-p9@DNASE1L3
Hg19::chr3:58196939..58196956,-p7@DNASE1L3
Hg19::chr7:158330204..158330217,+p2@ENST00000448698


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:0030128clathrin coat of endocytic vesicle0.00906548923612662
GO:0030669clathrin-coated endocytic vesicle membrane0.00906548923612662
GO:0030122AP-2 adaptor complex0.00906548923612662
GO:0030666endocytic vesicle membrane0.00906548923612662
GO:0045334clathrin-coated endocytic vesicle0.00906548923612662
GO:0030132clathrin coat of coated pit0.0124081634475196
GO:0006309DNA fragmentation during apoptosis0.0124081634475196
GO:0006921cell structure disassembly during apoptosis0.0124081634475196
GO:0030139endocytic vesicle0.0124081634475196
GO:0030125clathrin vesicle coat0.0124081634475196
GO:0030262apoptotic nuclear changes0.0124081634475196
GO:0030665clathrin coated vesicle membrane0.0124081634475196
GO:0006308DNA catabolic process0.0166393790457123
GO:0006997nuclear organization and biogenesis0.0166393790457123
GO:0005905coated pit0.0166393790457123
GO:0022411cellular component disassembly0.0166393790457123
GO:0030120vesicle coat0.0166393790457123
GO:0004536deoxyribonuclease activity0.0166393790457123
GO:0030662coated vesicle membrane0.0166393790457123
GO:0030131clathrin adaptor complex0.0166393790457123
GO:0030119AP-type membrane coat adaptor complex0.0166393790457123
GO:0030118clathrin coat0.0194091775309714
GO:0008632apoptotic program0.0250265430168767
GO:0030659cytoplasmic vesicle membrane0.0258598402874453
GO:0044433cytoplasmic vesicle part0.0258598402874453
GO:0012506vesicle membrane0.0258598402874453
GO:0030136clathrin-coated vesicle0.0258598402874453
GO:0030117membrane coat0.0258598402874453
GO:0048475coated membrane0.0258598402874453
GO:0030135coated vesicle0.0310077056707032
GO:0004519endonuclease activity0.0310077056707032
GO:0008565protein transporter activity0.0310077056707032
GO:0016043cellular component organization and biogenesis0.0310077056707032
GO:0010324membrane invagination0.0363450338784508
GO:0006897endocytosis0.0363450338784508
GO:0004518nuclease activity0.0440925552788139
GO:0016044membrane organization and biogenesis0.0495000262251407



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><br>

Cell Type
Ontology termp-valuen
endothelial cell of umbilical vein9.32e-173
vein endothelial cell1.25e-086
Uber Anatomy
Ontology termp-valuen
spleen2.12e-173
gastrointestinal system mesentery2.12e-173
stomach region2.12e-173
mesentery2.12e-173
gastrointestinal system serosa2.12e-173
mesentery of stomach2.12e-173
gut mesentery2.12e-173
dorsal mesentery2.12e-173
dorsal mesogastrium2.12e-173
peritoneal cavity2.12e-173
spleen primordium2.12e-173
umbilical vein2.90e-105
adult organism4.54e-10114
vein1.06e-099
venous blood vessel1.06e-099
venous system1.06e-099
abdomen element1.20e-0854
abdominal segment element1.20e-0854
mixed endoderm/mesoderm-derived structure2.16e-0829
hemopoietic organ9.99e-087
immune organ9.99e-087
intraembryonic coelom1.19e-0712
abdominal segment of trunk1.33e-0760
abdomen1.33e-0760
dura mater5.26e-071
future meninx5.26e-071
ectomeninx5.26e-071
future dura mater5.26e-071
endocrine gland6.07e-0735
stomach8.23e-078
food storage organ8.23e-078
mitral valve9.79e-071


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.11.57204
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.11.47594
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0022316
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.11.67751
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.11.36091
MA0115.11.21667
MA0116.12.13665
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.0127148
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.21.6882
MA0035.21.38583
MA0039.20.0170091
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0765396
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.21.2885e-05
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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

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.

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