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

Latest revision as of 11:53, 17 September 2013


Full id: C1825_pancreas_Hepatocyte_liver_colon_gastric_hepatoma_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr19:46367576..46367592,+p1@FOXA3
Hg19::chr1:199996702..199996732,+p5@NR5A2
Hg19::chr1:199996733..199996781,+p1@NR5A2
Hg19::chr6:107235378..107235418,-p1@ENST00000430094
Hg19::chrX:2882296..2882356,-p1@ARSE


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

p.valueFDRnGenesnPathwayName
2.20782089021958e-060.00139755062350899225Maturity onset diabetes of the young (KEGG):04950
4.73033289875392e-050.01497150362455622114Regulation of beta-cell development (Reactome):REACT_13698



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:0003702RNA polymerase II transcription factor activity0.0105280880666253
GO:0001678cell glucose homeostasis0.0105280880666253
GO:0042592homeostatic process0.0105280880666253
GO:0009267cellular response to starvation0.0105280880666253
GO:0031669cellular response to nutrient levels0.0105280880666253
GO:0004065arylsulfatase activity0.0105280880666253
GO:0042594response to starvation0.0105280880666253
GO:0031668cellular response to extracellular stimulus0.0105280880666253
GO:0042593glucose homeostasis0.0105280880666253
GO:0033554cellular response to stress0.0105280880666253
GO:0033500carbohydrate homeostasis0.0105280880666253
GO:0043565sequence-specific DNA binding0.0130242900715327
GO:0051716cellular response to stimulus0.0130242900715327
GO:0065008regulation of biological quality0.0130242900715327
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0130242900715327
GO:0008484sulfuric ester hydrolase activity0.0144693029843891
GO:0003704specific RNA polymerase II transcription factor activity0.016593720844225
GO:0031667response to nutrient levels0.0238504556699512
GO:0003700transcription factor activity0.0238504556699512
GO:0009991response to extracellular stimulus0.0238504556699512
GO:0048856anatomical structure development0.0383789720749396
GO:0003707steroid hormone receptor activity0.0383789720749396
GO:0007275multicellular organismal development0.0459567706342884
GO:0004879ligand-dependent nuclear receptor activity0.0459567706342884



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 cell3.73e-1712
endopolyploid cell3.73e-1712
parenchymal cell3.73e-1712
polyploid cell3.73e-1712
hepatocyte3.73e-1712
endodermal cell1.99e-0958
Uber Anatomy
Ontology termp-valuen
digestive tract diverticulum4.06e-2923
gastrointestinal system1.35e-2825
epithelium of foregut-midgut junction9.76e-2725
anatomical boundary9.76e-2725
hepatobiliary system9.76e-2725
foregut-midgut junction9.76e-2725
septum transversum9.76e-2725
hepatic diverticulum1.22e-2622
liver primordium1.22e-2622
sac2.58e-2526
intestine2.56e-2417
subdivision of digestive tract2.64e-23118
epithelial sac5.05e-2325
abdomen element9.75e-2054
abdominal segment element9.75e-2054
liver1.16e-1919
digestive gland1.16e-1919
liver bud1.16e-1919
gut epithelium1.88e-1954
digestive system8.74e-19145
digestive tract8.74e-19145
primitive gut8.74e-19145
abdominal segment of trunk3.06e-1760
abdomen3.06e-1760
endoderm-derived structure3.26e-16160
endoderm3.26e-16160
presumptive endoderm3.26e-16160
large intestine4.80e-1411
endo-epithelium7.89e-1482
trunk region element6.65e-13101
exocrine gland4.36e-1131
exocrine system4.36e-1131
small intestine4.76e-114
lower digestive tract9.80e-115
organ system subdivision1.35e-10223
foregut4.92e-1087
endocrine system5.85e-1045
mesenchyme7.20e-10160
entire embryonic mesenchyme7.20e-10160
endocrine gland1.52e-0935
colon3.49e-099
gland3.97e-0959
immaterial anatomical entity4.62e-09117
subdivision of trunk7.93e-09112
rectum4.67e-084
multi-tissue structure5.19e-08342
anatomical cluster1.33e-07373
trunk2.40e-07199
hindgut2.70e-0719
Disease
Ontology termp-valuen
adenocarcinoma8.78e-0925
carcinoma3.43e-08106
gastrointestinal system cancer1.08e-0714
signet ring cell adenocarcinoma1.67e-072
tubular adenocarcinoma1.90e-072


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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.14.05562
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.21.65235
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.11.66846
MA0153.11.21379
MA0154.10.98952
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.21.66926
MA0079.20.0442129
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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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