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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:35, 17 September 2013


Full id: C981_choriocarcinoma_chorionic_pancreatic_placenta_amniotic_vagina_MCF7



Phase1 CAGE Peaks

Hg19::chr10:71098164..71098182,+p@chr10:71098164..71098182
+
Hg19::chr10:8097468..8097478,+p16@GATA3
Hg19::chr1:161059803..161059816,-p7@PVRL4
Hg19::chr1:161059882..161059905,-p3@PVRL4
Hg19::chr1:161059935..161059942,-p@chr1:161059935..161059942
-
Hg19::chr2:228382337..228382369,+p@chr2:228382337..228382369
+
Hg19::chr5:80255192..80255201,+p@chr5:80255192..80255201
+
Hg19::chr9:112261641..112261646,+p@chr9:112261641..112261646
+


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:0042415norepinephrine metabolic process0.00350288472860002
GO:0042421norepinephrine biosynthetic process0.00350288472860002
GO:0048485sympathetic nervous system development0.00467044422881899
GO:0048483autonomic nervous system development0.00525417242194267
GO:0042423catecholamine biosynthetic process0.0140096828629117
GO:0042136neurotransmitter biosynthetic process0.0186779273270035
GO:0043627response to estrogen stimulus0.0198400389723906
GO:0006584catecholamine metabolic process0.0198400389723906
GO:0018958phenol metabolic process0.0198400389723906
GO:0001709cell fate determination0.0198400389723906
GO:0042133neurotransmitter metabolic process0.0198400389723906
GO:0042401biogenic amine biosynthetic process0.0198400389723906
GO:0048545response to steroid hormone stimulus0.019928932469712
GO:0042398amino acid derivative biosynthetic process0.0200707908551284
GO:0042446hormone biosynthetic process0.0200707908551284
GO:0042035regulation of cytokine biosynthetic process0.0248104870521948
GO:0042089cytokine biosynthetic process0.0248104870521948
GO:0042107cytokine metabolic process0.0248104870521948
GO:0045165cell fate commitment0.0248104870521948
GO:0006576biogenic amine metabolic process0.0248104870521948
GO:0009725response to hormone stimulus0.0248104870521948
GO:0001505regulation of neurotransmitter levels0.0248104870521948
GO:0042445hormone metabolic process0.0262372211764849
GO:0006575amino acid derivative metabolic process0.0262372211764849
GO:0001816cytokine production0.0316138775295708
GO:0009309amine biosynthetic process0.0320091784237637
GO:0050954sensory perception of mechanical stimulus0.032963518626922
GO:0007605sensory perception of sound0.032963518626922
GO:0044271nitrogen compound biosynthetic process0.0354356923500112
GO:0006725aromatic compound metabolic process0.0414706298862488
GO:0006417regulation of translation0.0414706298862488
GO:0031326regulation of cellular biosynthetic process0.0434401632898297
GO:0009889regulation of biosynthetic process0.0457994655493675
GO:0045893positive regulation of transcription, DNA-dependent0.0457994655493675



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
chorionic membrane mesenchymal stem cell1.41e-463
germ line cell2.32e-207
germ cell2.32e-207
extraembryonic cell3.48e-2019
amnion mesenchymal stem cell3.65e-135
Uber Anatomy
Ontology termp-valuen
acellular anatomical structure1.41e-463
egg chorion1.41e-463
extraembryonic membrane4.67e-3914
membranous layer4.67e-3914
chorion2.15e-357
extraembryonic structure9.22e-2324
amnion1.13e-097
somatic layer of lateral plate mesoderm1.42e-088
organ component layer3.86e-0866
Disease
Ontology termp-valuen
islet cell tumor1.04e-161
endocrine pancreas cancer1.04e-161
pancreatic endocrine carcinoma1.04e-161
germ cell and embryonal cancer7.03e-0722
germ cell cancer7.03e-0722


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)
MA0003.10.00718652
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.15.54305
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.11.93074
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0344109
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.12.13567
MA0084.11.42483
MA0087.10.885691
MA0088.10.441522
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.11.04489
MA0113.11.49247
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.11.38624
MA0139.10.155155
MA0140.10.516266
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.10.0613434
MA0146.10.0399277
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.21.28264
MA0039.20.00915579
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.10.627336
MA0080.21.48508
MA0018.20.599912
MA0099.20.523145
MA0079.20.00126912
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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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