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

Latest revision as of 11:37, 17 September 2013


Full id: C1088_liver_giant_anaplastic_glassy_bile_Hepatocyte_prostate



Phase1 CAGE Peaks

Hg19::chr6:64237703..64237708,+p@chr6:64237703..64237708
+
Hg19::chr6:64237756..64237769,+p@chr6:64237756..64237769
+
Hg19::chr6:64237780..64237794,+p@chr6:64237780..64237794
+
Hg19::chr6:64237801..64237820,+p@chr6:64237801..64237820
+
Hg19::chr6:64237829..64237843,+p@chr6:64237829..64237843
+
Hg19::chr6:64237863..64237874,+p@chr6:64237863..64237874
+
Hg19::chr6:64237875..64237910,+p@chr6:64237875..64237910
+
Hg19::chr6:64237919..64237932,+p@chr6:64237919..64237932
+


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>

Uber Anatomy
Ontology termp-valuen
larynx3.70e-189
endoderm-derived structure1.06e-15160
endoderm1.06e-15160
presumptive endoderm1.06e-15160
respiratory system2.16e-1374
exocrine gland2.74e-1231
exocrine system2.74e-1231
digestive system1.26e-11145
digestive tract1.26e-11145
primitive gut1.26e-11145
epithelium of foregut-midgut junction3.94e-1125
anatomical boundary3.94e-1125
hepatobiliary system3.94e-1125
foregut-midgut junction3.94e-1125
septum transversum3.94e-1125
gland6.56e-1159
hepatic diverticulum7.17e-1122
liver primordium7.17e-1122
gut epithelium1.06e-1054
foregut1.31e-1087
respiratory tract1.71e-1054
liver2.52e-1019
digestive gland2.52e-1019
liver bud2.52e-1019
digestive tract diverticulum2.64e-1023
upper respiratory tract8.13e-1019
endo-epithelium1.58e-0982
epithelial sac2.61e-0925
subdivision of digestive tract6.90e-09118
sac7.18e-0926
gingival epithelium9.69e-093
acellular anatomical structure1.08e-083
egg chorion1.08e-083
respiratory primordium1.20e-0738
endoderm of foregut1.20e-0738
endocrine gland2.70e-0735
skin gland6.47e-072
epidermis gland6.47e-072
gland of integumental system6.47e-072
sebaceous gland6.47e-072
skin sebaceous gland6.47e-072
sweat gland6.47e-072
sweat gland placode6.47e-072
sebaceous gland placode6.47e-072
mouth mucosa9.15e-0713
segment of respiratory tract9.57e-0747
Disease
Ontology termp-valuen
carcinoma1.25e-12106
cell type cancer3.65e-09143


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)
MA0003.10.00101002
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
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
MA0043.12.1209
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.12.22338
MA0072.10.888148
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.11.69066
MA0083.10.926258
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
MA0103.10.792149
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
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
MA0135.12.18252
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.14.51343
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.00761723
MA0147.10.243042
MA0148.10.480298
MA0149.11.26367
MA0062.20.161302
MA0035.20.515566
MA0039.20.00133745
MA0138.20.653421
MA0002.21.61227
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.13.17077
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.10.627336
MA0080.20.818924
MA0018.20.599912
MA0099.23.29548
MA0079.21.41562e-07
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467822.46317452600871.53751153688198e-111.87808382924464e-09
BHLHE40#8553844.87181354697746.04397679531981e-149.72614626388914e-12
BRCA1#672820.18423064322383.61942729088439e-114.1448395486039e-09
CEBPB#105187.971147625824826.12878626083745e-083.7987199305377e-06
ELF1#199784.258097958807549.24826870984006e-060.000246523720211074
EP300#203386.77394172622322.25366016107097e-071.19174690411185e-05
FOS#235388.99795530889442.32446530602145e-081.63808928539524e-06
FOSL2#2355816.93020060456171.47793326491323e-101.56545509385672e-08
FOXA1#3169811.08141974938554.39110036332964e-093.56057555004491e-07
FOXA2#3170824.63046375266527.35637804493982e-129.33527055450146e-10
GTF2F1#2962812.73966087675771.43868108630934e-091.2831290689416e-07
HDAC2#3066813.41562023662639.51254966654288e-108.87036763057207e-08
HEY1#2346284.040111043105711.4081650274634e-050.000339255703121685
HNF4A#3172823.13229036295371.21561011047446e-111.50959695990299e-09
JUN#3725812.51282919233631.66110954195842e-091.45662988625185e-07
JUND#372786.994663941871031.74369580801501e-079.57968682237137e-06
MAX#414986.452555509007123.32496617557502e-071.65992419890478e-05
NR3C1#2908814.9730233311733.9500670680339e-103.89557180848341e-08
POLR2A#543082.147453176558070.002210725788971910.0127251978987234
RAD21#5885810.35503389545637.55391711153941e-095.84821014982998e-07
RXRA#6256820.07461713913333.7806502647693e-114.31999270243152e-09
SMARCC1#6599843.66335931963157.52062965894322e-141.19187714863486e-11
SMC3#9126815.04493284493283.80148882898722e-103.77398946588019e-08
SP1#666785.69838137814098.98832477855329e-073.86627533586214e-05
SPI1#668866.153242631392047.3612205654473e-050.00114866056272934
STAT1#6772820.70658749719922.95008695392417e-113.42718722336915e-09
STAT3#6774810.51946499715426.65923543127245e-095.22527339749559e-07
TBP#690883.706770687096392.80450451364125e-050.000592434560882237
TCF7L2#6934810.77017656313735.51536816569572e-094.40381908147626e-07
TRIM28#10155818.59052504526256.99051420669847e-117.70129022398082e-09
USF1#739186.361499277207963.72538670743375e-071.83353281026236e-05



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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