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{{Coexpression_clusters
{
|full_id=C611_small_hepatocellular_colon_adenocarcinoma_Intestinal_signet_temporal
|

Latest revision as of 11:26, 17 September 2013


Full id: C611_small_hepatocellular_colon_adenocarcinoma_Intestinal_signet_temporal



Phase1 CAGE Peaks

Hg19::chr10:102729876..102729890,-p1@AK000735
Hg19::chr10:102729908..102729938,-p2@AK000735
Hg19::chr13:76335013..76335032,+p14@LMO7
Hg19::chr16:2034715..2034726,+p10@GFER
Hg19::chr16:75284758..75284802,-p@chr16:75284758..75284802
-
Hg19::chr2:233742013..233742020,-p@chr2:233742013..233742020
-
Hg19::chr2:61245275..61245310,-p6@PUS10
Hg19::chr2:74753294..74753302,-p6@DQX1
Hg19::chr2:74753305..74753331,-p2@DQX1
Hg19::chr2:74753332..74753373,-p1@DQX1
Hg19::chr3:8693755..8693789,-p1@C3orf32
Hg19::chr6:158993336..158993351,+p10@TMEM181
Hg19::chr7:55256663..55256679,-p2@ENST00000442411
p2@uc003tqo.2
Hg19::chr9:86571432..86571453,-p5@C9orf64


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:0016972thiol oxidase activity0.0141274113637933
GO:0016670oxidoreductase activity, acting on sulfur group of donors, oxygen as acceptor0.0141274113637933



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
intestinal epithelial cell2.36e-094
metabolising cell4.59e-0712
endopolyploid cell4.59e-0712
parenchymal cell4.59e-0712
polyploid cell4.59e-0712
hepatocyte4.59e-0712
Uber Anatomy
Ontology termp-valuen
intestine9.34e-3717
gastrointestinal system7.88e-3125
colon3.27e-239
large intestine5.57e-1911
small intestine4.04e-164
subdivision of digestive tract2.65e-13118
digestive system5.89e-12145
digestive tract5.89e-12145
primitive gut5.89e-12145
endoderm-derived structure1.41e-10160
endoderm1.41e-10160
presumptive endoderm1.41e-10160
vermiform appendix1.48e-091
caecum1.48e-091
midgut1.48e-091
intestinal mucosa2.36e-094
wall of intestine2.36e-094
gastrointestinal system mucosa2.36e-094
gastrointestinal system epithelium2.36e-094
intestinal epithelium2.36e-094
nucleus accumbens2.67e-091
ventral striatum2.67e-091
digestive tract diverticulum4.59e-0923
gut epithelium6.13e-0954
epithelium of foregut-midgut junction2.41e-0825
anatomical boundary2.41e-0825
hepatobiliary system2.41e-0825
foregut-midgut junction2.41e-0825
septum transversum2.41e-0825
sac5.37e-0826
organ system subdivision1.05e-07223
lower digestive tract1.66e-075
liver2.26e-0719
digestive gland2.26e-0719
liver bud2.26e-0719


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)
MA0003.10.306921
MA0004.10.275994
MA0006.10.464315
MA0007.10.7221
MA0009.10.695988
MA0014.10.298852
MA0017.14.76359
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.492785
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.11.64005
MA0048.10.499624
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.10.276748
MA0056.10
MA0057.10.10396
MA0058.10.200063
MA0059.10.199079
MA0060.10.0773489
MA0061.10.224865
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.0444239
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.0345424
MA0074.10.943486
MA0076.10.609177
MA0077.10.65962
MA0078.10.447828
MA0081.10.578007
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.752017
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.691297
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.448026
MA0105.10.0899037
MA0106.12.73107
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.11.06479
MA0114.13.68475
MA0115.10.929032
MA0116.10.354243
MA0117.10.732
MA0119.10.18693
MA0122.11.78784
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.966693
MA0139.10.206516
MA0140.10.327488
MA0141.10.574537
MA0142.10.514195
MA0143.11.8739
MA0144.10.652118
MA0145.10.16253
MA0146.10.382098
MA0147.10.111828
MA0148.10.804328
MA0149.10.319221
MA0062.21.2433
MA0035.20.326883
MA0039.22.09143
MA0138.21.99066
MA0002.20.0708857
MA0137.20.504333
MA0104.20.0769208
MA0047.21.00935
MA0112.20.150022
MA0065.21.57252
MA0150.10.624926
MA0151.10
MA0152.10.886132
MA0153.11.8578
MA0154.11.39905
MA0155.10.486086
MA0156.10.508404
MA0157.10.489002
MA0158.10
MA0159.10.361202
MA0160.10.30953
MA0161.10
MA0162.10.287126
MA0163.10.0498121
MA0164.10.425415
MA0080.20.915505
MA0018.20.400879
MA0099.20.333432
MA0079.20.211527
MA0102.21.22472
MA0258.10.624652
MA0259.10.753086
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
CEBPB#105163.416206125353490.004751768568105380.0223343815249486
ELF1#199792.737348687804850.001336570728112650.00886962195154133
EP300#203383.870823843556110.0002923517603882410.00310262427631212
FOSL2#235544.837200172731910.007541622873992410.0310877625251379
FOXA1#316997.123769838890655.19704363903544e-072.42743309757255e-05
FOXA2#3170712.31523187633264.83510549852797e-072.27876165686265e-05
HDAC2#306687.666068706643581.89551452608875e-066.97799230138115e-05
HEY1#23462144.040111043105713.23477172841824e-092.67487192829986e-07
HNF4A#31721219.82767745396033.54543106940285e-156.31879309654204e-13
HNF4G#3174918.48434305271581.26472046417331e-101.35612053960777e-08
NR2C2#718249.318460258640250.0006903631933539260.00556548371676501
POLR2A#5430142.147453176558072.25331953374171e-050.000492434481658192
RXRA#6256912.90511101801422.9964879042402e-092.51163884615523e-07
SIN3A#2594293.477140181524020.0002040865328013360.00242211288627713
SP1#666793.663245171662010.0001341814525306330.00175941955063989
SRF#672254.927563665059930.002294485564587050.0130179149217681
TAF1#6872102.387890204103780.00162422337608950.010167971298652
TBP#690892.382924013133390.003811761126235160.0188243105855341
TCF7L2#693475.385088281568670.0001130226217794280.00154887411048703



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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