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Coexpression cluster:C4521: Difference between revisions

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{{Coexpression_clusters
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|ontology_enrichment_celltype=CL:0000066!8.34e-24!254;CL:0002321!7.54e-20!248;CL:0000220!4.03e-19!246;CL:0002076!2.68e-14!43;CL:0000223!3.17e-14!59;CL:0000359!1.21e-07!32;CL:0000192!4.56e-07!42;CL:0000514!4.56e-07!42;CL:0002368!7.72e-07!13;CL:0000393!8.63e-07!60;CL:0000211!8.63e-07!60
|ontology_enrichment_disease=DOID:193!1.38e-11!29;DOID:120!1.85e-10!27;DOID:2394!5.11e-09!14;DOID:305!2.20e-07!106
|ontology_enrichment_uberon=UBERON:0003914!3.81e-19!118;UBERON:0000922!1.46e-14!612;UBERON:0004119!3.67e-14!169;UBERON:0000925!3.67e-14!169;UBERON:0006595!3.67e-14!169;UBERON:0004111!1.64e-13!241;UBERON:0002050!1.04e-12!605;UBERON:0005423!1.04e-12!605;UBERON:0004535!1.04e-12!110;UBERON:0000923!1.12e-12!604;UBERON:0005291!1.12e-12!604;UBERON:0006598!1.12e-12!604;UBERON:0002532!1.12e-12!604;UBERON:0001009!1.33e-12!113;UBERON:0000466!1.88e-12!126;UBERON:0000467!6.79e-12!625;UBERON:0002049!6.83e-12!79;UBERON:0007798!6.83e-12!79;UBERON:0000480!6.89e-12!626;UBERON:0000477!6.98e-12!286;UBERON:0000468!1.30e-11!659;UBERON:0001007!1.48e-11!155;UBERON:0001555!1.48e-11!155;UBERON:0007026!1.48e-11!155;UBERON:0000481!3.33e-11!347;UBERON:0000464!3.73e-11!104;UBERON:0003104!6.20e-11!238;UBERON:0009142!6.20e-11!238;UBERON:0001637!1.01e-10!42;UBERON:0003509!1.01e-10!42;UBERON:0004572!1.01e-10!42;UBERON:0001048!1.35e-10!168;UBERON:0000490!1.64e-10!138;UBERON:0000926!2.49e-10!448;UBERON:0004120!2.49e-10!448;UBERON:0006603!2.49e-10!448;UBERON:0004921!3.24e-10!129;UBERON:0004185!3.24e-10!129;UBERON:0005156!7.25e-10!59;UBERON:0000990!7.25e-10!59;UBERON:0006554!7.98e-10!44;UBERON:0004872!8.09e-10!84;UBERON:0000055!1.05e-09!69;UBERON:0001008!1.17e-09!45;UBERON:0003103!1.82e-09!69;UBERON:0001981!3.66e-09!60;UBERON:0007500!3.66e-09!60;UBERON:0004537!3.66e-09!60;UBERON:0006965!3.66e-09!60;UBERON:0002553!7.78e-09!70;UBERON:0005911!1.19e-08!82;UBERON:0003886!2.30e-08!63;UBERON:0000483!3.04e-08!309;UBERON:0000025!3.04e-08!194;UBERON:0000119!3.39e-08!312;UBERON:0000077!3.47e-08!130;UBERON:0004573!3.67e-08!33;UBERON:0004571!3.67e-08!33;UBERON:0003133!3.69e-08!48;UBERON:0003100!3.92e-08!41;UBERON:0004176!6.01e-08!22;UBERON:0000992!1.23e-07!13;UBERON:0002100!1.28e-07!216;UBERON:0000991!1.42e-07!21;UBERON:0009196!1.42e-07!21;UBERON:0009117!1.42e-07!21;UBERON:0005564!1.42e-07!21;UBERON:0005177!1.61e-07!107;UBERON:0003134!3.59e-07!37;UBERON:0000474!3.59e-07!37;UBERON:0000058!6.06e-07!26
}}

Latest revision as of 14:14, 17 September 2013


Full id: C4521_bile_mesenchymal_meningioma_alveolar_Wilms_Small_prostate



Phase1 CAGE Peaks

Hg19::chr5:76114847..76114867,+p1@F2RL1
Hg19::chr5:76114872..76114892,+p2@F2RL1
Hg19::chr5:76114932..76114943,+p4@F2RL1


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
epithelial tube1.01e-18117
anatomical cluster6.14e-16373
endoderm-derived structure4.03e-14160
endoderm4.03e-14160
presumptive endoderm4.03e-14160
embryo1.01e-12592
cardiovascular system1.43e-12109
circulatory system1.71e-12112
anatomical conduit2.80e-12240
anatomical system1.07e-11624
anatomical group1.17e-11625
vasculature1.20e-1178
vascular system1.20e-1178
digestive system2.72e-11145
digestive tract2.72e-11145
primitive gut2.72e-11145
developing anatomical structure3.28e-11581
urinary system structure4.54e-1147
organism subdivision6.03e-11264
multi-cellular organism6.42e-11656
renal system7.22e-1148
immaterial anatomical entity1.19e-10117
artery2.22e-1042
arterial blood vessel2.22e-1042
arterial system2.22e-1042
subdivision of digestive tract2.26e-10118
reproductive structure3.76e-1059
reproductive system3.76e-1059
compound organ4.61e-1068
splanchnic layer of lateral plate mesoderm6.81e-1083
vessel1.67e-0968
primordium2.18e-09160
anatomical space2.29e-0995
multi-tissue structure2.87e-09342
endo-epithelium2.95e-0982
epithelial tube open at both ends3.38e-0959
blood vessel3.38e-0959
blood vasculature3.38e-0959
vascular cord3.38e-0959
trunk1.17e-08199
trunk region element1.21e-08101
female organism1.48e-0841
reproductive organ2.73e-0848
epithelium4.13e-08306
cell layer4.52e-08309
external genitalia4.71e-0822
unilaminar epithelium4.88e-08148
embryonic structure6.09e-08564
systemic artery8.24e-0833
systemic arterial system8.24e-0833
female gonad1.06e-0713
gonad1.10e-0721
indifferent external genitalia1.10e-0721
indifferent gonad1.10e-0721
gonad primordium1.10e-0721
tube1.46e-07192
female reproductive organ2.17e-0737
female reproductive system2.17e-0737
mesenchyme3.01e-07160
entire embryonic mesenchyme3.01e-07160
germ layer3.57e-07560
germ layer / neural crest3.57e-07560
embryonic tissue3.57e-07560
presumptive structure3.57e-07560
germ layer / neural crest derived structure3.57e-07560
epiblast (generic)3.57e-07560
Disease
Ontology termp-valuen
reproductive organ cancer1.54e-1129
female reproductive organ cancer2.04e-1027
ovarian cancer7.94e-0914
carcinoma8.69e-08106


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
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
MA0048.15.4446
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
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
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.11.5295
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.14.12243
MA0143.12.29531
MA0144.12.26598
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.22.70092
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
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
CTCF#1066435.360256373075030.0064925092527670.0280984242437317
E2F1#186934.907389214879320.008460985347239390.0327256073135447
E2F6#187635.017155731697390.00791769806886330.032395066544465
EP300#203336.77394172622320.003216880500103790.0168194133942598
FOXA2#3170324.63046375266526.68983856509345e-050.00107588550954696
HDAC2#3066313.41562023662630.0004140761399857210.00392999799927015
NANOG#79923329.24477848101273.99627955670032e-050.000740275701706678
NR3C1#2908314.9730233311730.0002978331194675480.00309907274724233
NRF1#4899312.21027944771090.0005492172401020010.00472991666026329
STAT3#6774310.51946499715420.0008589184530415310.00644985507026204
TAF7#6879311.43306940492390.0006690181981945830.00545147784982789
TCF12#6938310.63446490218640.0008313523990202070.00631504932731627
TCF7L2#6934310.77017656313730.0008003181298398380.00616768190395092
ZNF263#1012738.221841637010680.001799043925565870.010994812367147



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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