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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:42, 17 September 2013


Full id: C1339_small_colon_signet_trachea_gall_adenocarcinoma_Renal



Phase1 CAGE Peaks

Hg19::chr11:2925001..2925048,-p4@SLC22A18AS
Hg19::chr3:168991226..168991244,-p@chr3:168991226..168991244
-
Hg19::chr6:31846768..31846780,-p1@SLC44A4
Hg19::chr9:130877529..130877536,-p@chr9:130877529..130877536
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Hg19::chr9:130877564..130877577,-p@chr9:130877564..130877577
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Hg19::chr9:130877614..130877619,-p@chr9:130877614..130877619
-


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

No GOStat results

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
epithelial cell of stomach3.44e-073
Uber Anatomy
Ontology termp-valuen
gastrointestinal system5.14e-3825
intestine1.75e-3017
large intestine1.29e-2011
subdivision of digestive tract1.99e-20118
digestive system1.48e-18145
digestive tract1.48e-18145
primitive gut1.48e-18145
endoderm-derived structure1.21e-17160
endoderm1.21e-17160
presumptive endoderm1.21e-17160
lower digestive tract2.87e-155
colon2.13e-139
rectum5.71e-114
organ system subdivision1.27e-10223
gut epithelium1.30e-0954
small intestine1.67e-094
stomach2.11e-098
food storage organ2.11e-098
digestive tract diverticulum7.76e-0923
multi-tissue structure3.21e-08342
hindgut3.27e-0819
epithelium of foregut-midgut junction4.97e-0825
anatomical boundary4.97e-0825
hepatobiliary system4.97e-0825
foregut-midgut junction4.97e-0825
septum transversum4.97e-0825
adult organism9.54e-08114
sac1.04e-0726
gland5.37e-0759
anatomical cluster7.25e-07373
hepatic diverticulum8.04e-0722
liver primordium8.04e-0722
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma9.41e-112
gastrointestinal system cancer5.38e-0814


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)
MA0003.10.176622
MA0004.11.37419
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.15.7156
MA0056.10
MA0057.11.41984
MA0058.14.08025
MA0059.12.99917
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.120085
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.12.7063
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.11.76074
MA0105.10.419295
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.12.62599
MA0140.11.50842
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.70894
MA0146.11.8938
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.21.22729
MA0035.20.621793
MA0039.20.200862
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.332548
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.11.57484
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.0318308
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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
ATF3#467311.23158726300440.001593459971184230.0100391727049834
BHLHE40#8553322.43590677348870.0002103196104780280.00244632696277032
FOSL2#235538.465100302280850.003598315634615090.0182199401999208
FOXA1#316935.540709874692730.01192178777860280.0433757043654241
FOXA2#3170312.31523187633260.001219712440124520.0082046597664669
GATA1#262336.780154071900220.006765763983348560.0287461708090371
GATA2#262436.3724658667770.008058821308742550.0318832956536012
HDAC2#306636.707810118313130.006973940027962660.0294855203052543
HNF4A#3172311.56614518147680.001463487150085730.0093764268736767
HNF4G#3174314.37671126322340.0007769772937197380.00608981100028486
RXRA#6256310.03730856956660.002205419116789220.0127051556698301
SMARCA4#6597252.25530110262930.0005995659215741950.00500944522266299
TCF12#693835.317232451093210.013367345733860.0472412094307865
TCF7L2#693435.385088281568670.01290488779931040.0464013487871712
USF2#739236.49609869253480.007634319815300560.0314537349477366



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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