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{{Coexpression_clusters
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|full_id=C4738_signet_lung_Intestinal_hepatoma_Hepatocyte_Prostate_pineal
|id=C4738
|ontology_enrichment_celltype=CL:0000066!1.71e-14!254;CL:0000223!1.78e-10!59
|ontology_enrichment_disease=DOID:305!2.49e-25!106;DOID:0050687!1.26e-24!143;DOID:162!3.51e-12!235;DOID:14566!5.02e-11!239;DOID:299!9.79e-08!25
|ontology_enrichment_uberon=UBERON:0007023!1.08e-34!115;UBERON:0001007!3.93e-22!155;UBERON:0001555!3.93e-22!155;UBERON:0007026!3.93e-22!155;UBERON:0004119!7.44e-21!169;UBERON:0000925!7.44e-21!169;UBERON:0006595!7.44e-21!169;UBERON:0004921!1.27e-19!129;UBERON:0004185!1.27e-19!129;UBERON:0000062!3.54e-17!511;UBERON:0000481!6.34e-16!347;UBERON:0000077!1.10e-15!130;UBERON:0002346!3.30e-14!90;UBERON:0003075!4.28e-14!86;UBERON:0007284!4.28e-14!86;UBERON:0000153!5.01e-14!129;UBERON:0007811!5.01e-14!129;UBERON:0000033!7.20e-14!123;UBERON:0001049!2.37e-13!57;UBERON:0005068!2.37e-13!57;UBERON:0006241!2.37e-13!57;UBERON:0007135!2.37e-13!57;UBERON:0000477!5.86e-13!286;UBERON:0000924!7.34e-13!173;UBERON:0006601!7.34e-13!173;UBERON:0004121!1.28e-12!169;UBERON:0001041!4.25e-12!98;UBERON:0005743!9.43e-12!86;UBERON:0000073!1.36e-11!94;UBERON:0001016!1.36e-11!94;UBERON:0003056!5.40e-11!61;UBERON:0001017!5.43e-11!82;UBERON:0003080!5.69e-11!42;UBERON:0000064!7.07e-11!219;UBERON:0000468!7.66e-11!659;UBERON:0000922!9.17e-11!612;UBERON:0005911!9.29e-11!82;UBERON:0000955!1.02e-10!69;UBERON:0006238!1.02e-10!69;UBERON:0004111!1.54e-10!241;UBERON:0002616!1.56e-10!59;UBERON:0002780!1.77e-10!41;UBERON:0001890!1.77e-10!41;UBERON:0006240!1.77e-10!41;UBERON:0003929!6.89e-10!54;UBERON:0001048!8.24e-10!168;UBERON:0000467!9.63e-10!625;UBERON:0002050!1.25e-09!605;UBERON:0005423!1.25e-09!605;UBERON:0000480!1.40e-09!626;UBERON:0000923!1.96e-09!604;UBERON:0005291!1.96e-09!604;UBERON:0006598!1.96e-09!604;UBERON:0002532!1.96e-09!604;UBERON:0009497!9.16e-09!25;UBERON:0000015!9.16e-09!25;UBERON:0002423!9.16e-09!25;UBERON:0006235!9.16e-09!25;UBERON:0004161!9.16e-09!25;UBERON:0002530!1.96e-08!59;UBERON:0001004!2.40e-08!72;UBERON:0000161!3.71e-08!35;UBERON:0000475!5.89e-08!365;UBERON:0002020!6.52e-08!34;UBERON:0003528!6.52e-08!34;UBERON:0001893!1.04e-07!34;UBERON:0002791!1.76e-07!33;UBERON:0005409!1.86e-07!35;UBERON:0009854!2.10e-07!23;UBERON:0001869!3.86e-07!32;UBERON:0008835!4.03e-07!22;UBERON:0003894!4.03e-07!22;UBERON:0000483!5.07e-07!309;UBERON:0000466!7.35e-07!126;UBERON:0009856!8.75e-07!26;UBERON:0000119!9.20e-07!312
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4738_signet_lung_Intestinal_hepatoma_Hepatocyte_Prostate_pineal



Phase1 CAGE Peaks

Hg19::chr8:17658596..17658611,-p2@MTUS1
Hg19::chr8:17658625..17658646,-p4@MTUS1
Hg19::chr8:17658681..17658691,-p11@MTUS1


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 cell7.48e-12253
endodermal cell1.41e-1158
epithelial cell of alimentary canal9.80e-0720
Uber Anatomy
Ontology termp-valuen
adult organism7.05e-36114
organ system subdivision8.31e-28223
digestive system2.52e-21145
digestive tract2.52e-21145
primitive gut2.52e-21145
endoderm-derived structure2.62e-20160
endoderm2.62e-20160
presumptive endoderm2.62e-20160
subdivision of digestive tract9.38e-20118
anatomical cluster5.97e-19373
multi-tissue structure1.01e-15342
organ1.91e-13503
foregut1.23e-1287
neural tube1.36e-1256
neural rod1.36e-1256
future spinal cord1.36e-1256
neural keel1.36e-1256
neurectoderm8.44e-1286
gut epithelium9.14e-1254
neural plate1.69e-1182
presumptive neural plate1.69e-1182
regional part of nervous system1.82e-1153
regional part of brain1.82e-1153
endo-epithelium3.18e-1182
anatomical conduit3.69e-10240
ecto-epithelium4.23e-10104
regional part of forebrain5.45e-1041
forebrain5.45e-1041
anterior neural tube5.45e-1041
future forebrain5.45e-1041
central nervous system6.22e-1081
nervous system7.35e-1089
brain7.63e-1068
future brain7.63e-1068
epithelium of foregut-midgut junction2.45e-0925
anatomical boundary2.45e-0925
hepatobiliary system2.45e-0925
foregut-midgut junction2.45e-0925
septum transversum2.45e-0925
primordium4.98e-09160
ectoderm-derived structure5.51e-09171
ectoderm5.51e-09171
presumptive ectoderm5.51e-09171
pre-chordal neural plate9.58e-0961
organ part1.11e-08218
gland2.46e-0859
multi-cellular organism3.00e-08656
orifice6.07e-0836
digestive tract diverticulum7.11e-0823
hepatic diverticulum1.01e-0722
liver primordium1.01e-0722
brain grey matter1.94e-0734
gray matter1.94e-0734
immaterial anatomical entity1.99e-07117
embryo2.36e-07592
telencephalon2.54e-0734
gastrointestinal system2.90e-0725
respiratory system3.27e-0774
hindgut6.20e-0719
developing anatomical structure7.16e-07581
endocrine gland7.40e-0735
anatomical system8.08e-07624
cerebral hemisphere8.68e-0732
sac9.01e-0726
regional part of telencephalon9.35e-0732
Disease
Ontology termp-valuen
carcinoma6.92e-27106
cell type cancer5.56e-26143
cancer1.79e-13235
disease of cellular proliferation2.11e-12239
adenocarcinoma6.65e-0825
squamous cell carcinoma1.23e-0714


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)
MA0003.15.30359
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.14.7105
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.16.29415
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.21.34467
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.25.72079
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
E2F1#186934.907389214879320.008460985347239390.0327875347363858
E2F4#1874312.66806031528440.0004917987006298980.00439074752052368
EP300#203336.77394172622320.003216880500103790.0168548528846807
FOXA1#3169311.08141974938550.000734755275698670.00584352012174028
FOXA2#3170324.63046375266526.68983856509345e-050.00107721253453561
HDAC2#3066313.41562023662630.0004140761399857210.00393679544687926
HNF4A#3172323.13229036295378.07584663437677e-050.00123489509026014
HNF4G#3174328.75342252644684.20470658818262e-050.000760802757039509
NR3C1#2908314.9730233311730.0002978331194675480.00310371115187301
RXRA#6256320.07461713913330.0001235730348432220.00166034274874454
SP1#666735.69838137814090.005403962701712170.0247993874946883
STAT3#6774310.51946499715420.0008589184530415310.00645914345601991
TCF7L2#6934310.77017656313730.0008003181298398380.00617679760289262
TFAP2A#7020316.5186343730450.0002218033880766340.00249541355675273
TFAP2C#7022310.80922860986020.0007916746575753130.006190604190065



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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