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{{Coexpression_clusters
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|full_id=C4739_heart_vagina_bile_pineal_pancreas_lung_bladder
|id=C4739
|ontology_enrichment_celltype=CL:0000066!1.39e-12!254;CL:0000223!2.18e-09!59;CL:0002076!5.94e-07!43
|ontology_enrichment_disease=DOID:305!5.62e-20!106;DOID:0050687!3.32e-18!143;DOID:299!1.05e-07!25;DOID:162!7.15e-07!235
|ontology_enrichment_uberon=UBERON:0007023!8.41e-40!115;UBERON:0000062!1.21e-24!511;UBERON:0001007!1.10e-21!155;UBERON:0001555!1.10e-21!155;UBERON:0007026!1.10e-21!155;UBERON:0004119!3.61e-21!169;UBERON:0000925!3.61e-21!169;UBERON:0006595!3.61e-21!169;UBERON:0000481!3.34e-20!347;UBERON:0004921!1.65e-18!129;UBERON:0004185!1.65e-18!129;UBERON:0000033!4.94e-18!123;UBERON:0000153!5.41e-18!129;UBERON:0007811!5.41e-18!129;UBERON:0002346!5.82e-17!90;UBERON:0003075!1.04e-16!86;UBERON:0007284!1.04e-16!86;UBERON:0001049!2.27e-16!57;UBERON:0005068!2.27e-16!57;UBERON:0006241!2.27e-16!57;UBERON:0007135!2.27e-16!57;UBERON:0000468!1.82e-15!659;UBERON:0005743!4.17e-15!86;UBERON:0000924!4.19e-15!173;UBERON:0006601!4.19e-15!173;UBERON:0000922!5.61e-15!612;UBERON:0000077!7.37e-15!130;UBERON:0004121!9.91e-15!169;UBERON:0000064!1.23e-14!219;UBERON:0001017!2.10e-14!82;UBERON:0000955!4.49e-14!69;UBERON:0006238!4.49e-14!69;UBERON:0000467!5.79e-14!625;UBERON:0002050!6.55e-14!605;UBERON:0005423!6.55e-14!605;UBERON:0000073!9.02e-14!94;UBERON:0001016!9.02e-14!94;UBERON:0000480!9.49e-14!626;UBERON:0000477!1.08e-13!286;UBERON:0000923!1.30e-13!604;UBERON:0005291!1.30e-13!604;UBERON:0006598!1.30e-13!604;UBERON:0002532!1.30e-13!604;UBERON:0002616!2.01e-13!59;UBERON:0000475!6.49e-13!365;UBERON:0003080!3.22e-12!42;UBERON:0003056!5.11e-12!61;UBERON:0002780!1.04e-11!41;UBERON:0001890!1.04e-11!41;UBERON:0006240!1.04e-11!41;UBERON:0001041!1.39e-11!98;UBERON:0004111!2.59e-11!241;UBERON:0001048!2.32e-10!168;UBERON:0001004!6.79e-10!72;UBERON:0005911!8.25e-10!82;UBERON:0000466!1.73e-09!126;UBERON:0000483!4.88e-09!309;UBERON:0000161!5.88e-09!35;UBERON:0002530!7.33e-09!59;UBERON:0000119!7.48e-09!312;UBERON:0002020!9.70e-09!34;UBERON:0003528!9.70e-09!34;UBERON:0001893!1.54e-08!34;UBERON:0003929!2.52e-08!54;UBERON:0002791!2.85e-08!33;UBERON:0005177!4.16e-08!107;UBERON:0000063!6.82e-08!97;UBERON:0001869!1.44e-07!32;UBERON:0009497!6.74e-07!25;UBERON:0000015!6.74e-07!25;UBERON:0002423!6.74e-07!25;UBERON:0006235!6.74e-07!25;UBERON:0004161!6.74e-07!25;UBERON:0002619!7.29e-07!22
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4739_heart_vagina_bile_pineal_pancreas_lung_bladder



Phase1 CAGE Peaks

Hg19::chr8:17658704..17658715,-p10@MTUS1
Hg19::chr8:17658721..17658766,-p3@MTUS1
Hg19::chr8:17658793..17658804,-p9@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
endodermal cell1.02e-0958
epithelial cell2.17e-09253
epithelial cell of alimentary canal2.94e-0720
endo-epithelial cell3.81e-0742
Uber Anatomy
Ontology termp-valuen
adult organism7.72e-43114
organ system subdivision5.44e-30223
digestive system3.91e-23145
digestive tract3.91e-23145
primitive gut3.91e-23145
endoderm-derived structure6.43e-23160
endoderm6.43e-23160
presumptive endoderm6.43e-23160
anatomical cluster1.63e-20373
multi-tissue structure2.84e-20342
subdivision of digestive tract3.19e-20118
organ2.02e-19503
neural tube1.21e-1556
neural rod1.21e-1556
future spinal cord1.21e-1556
neural keel1.21e-1556
neurectoderm2.25e-1486
neural plate2.90e-1482
presumptive neural plate2.90e-1482
regional part of nervous system4.79e-1453
regional part of brain4.79e-1453
organ part6.30e-13218
foregut6.58e-1387
ecto-epithelium9.06e-12104
regional part of forebrain9.26e-1241
forebrain9.26e-1241
anterior neural tube9.26e-1241
future forebrain9.26e-1241
anatomical conduit2.71e-11240
brain2.94e-1168
future brain2.94e-1168
ectoderm-derived structure3.05e-11171
ectoderm3.05e-11171
presumptive ectoderm3.05e-11171
central nervous system5.19e-1181
respiratory system1.31e-1074
nervous system1.79e-1089
multi-cellular organism2.78e-10656
pre-chordal neural plate2.83e-1061
orifice5.08e-1036
endo-epithelium5.23e-1082
anatomical system9.98e-10624
embryo1.31e-09592
anatomical group1.36e-09625
developing anatomical structure1.53e-09581
primordium6.67e-09160
embryonic structure7.17e-09564
structure with developmental contribution from neural crest1.50e-08132
gut epithelium1.58e-0854
germ layer2.14e-08560
germ layer / neural crest2.14e-08560
embryonic tissue2.14e-08560
presumptive structure2.14e-08560
germ layer / neural crest derived structure2.14e-08560
epiblast (generic)2.14e-08560
brain grey matter2.14e-0834
gray matter2.14e-0834
immaterial anatomical entity2.33e-08117
telencephalon4.46e-0834
gland9.24e-0859
gastrointestinal system1.56e-0725
regional part of telencephalon2.15e-0732
cerebral hemisphere4.44e-0732
oral opening5.08e-0722
Disease
Ontology termp-valuen
carcinoma1.53e-19106
cell type cancer4.28e-17143
adenocarcinoma3.69e-0725
cancer4.30e-07235
squamous cell carcinoma5.09e-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)
MA0003.16.06693
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
MA0048.10.341392
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
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
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
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
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
MA0145.10.752137
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.13.19371
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.10519
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#186934.907389214879320.008460985347239390.0327887513424985
E2F4#1874312.66806031528440.0004917987006298980.00439112289433923
E2F6#187635.017155731697390.00791769806886330.0324484566243138
EP300#203336.77394172622320.003216880500103790.0168556985024252
FOXA1#3169311.08141974938550.000734755275698670.00584396513888457
FOXA2#3170324.63046375266526.68983856509345e-050.00107737864286784
HDAC2#3066313.41562023662630.0004140761399857210.00393715385870072
HNF4A#3172323.13229036295378.07584663437677e-050.00123507592128815
HNF4G#3174328.75342252644684.20470658818262e-050.000760934589088901
MXI1#460139.96157162875930.001011470541259020.0072373918784976
NR3C1#2908314.9730233311730.0002978331194675480.00310402087257472
RXRA#6256320.07461713913330.0001235730348432220.00166055638008123
SP1#666735.69838137814090.005403962701712170.0248004772423482
STAT3#6774310.51946499715420.0008589184530415310.00645960857760528
TCF7L2#6934310.77017656313730.0008003181298398380.00617725409521416
TFAP2A#7020316.5186343730450.0002218033880766340.00249568240113506
TFAP2C#7022310.80922860986020.0007916746575753130.00619106773212341



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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