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{{Coexpression_clusters
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|full_id=C3226_Endothelial_hepatic_Renal_Urothelial_Ewing_Preadipocyte_Fibroblast
|id=C3226
|ontology_enrichment_celltype=CL:0000222!1.83e-12!119;CL:0002139!1.85e-11!24;CL:0000220!8.20e-11!246;CL:0002321!1.13e-10!248;CL:0000213!1.20e-09!57;CL:0000215!1.20e-09!57;CL:0000115!4.19e-09!35;CL:0002078!2.36e-08!44;CL:0000071!7.08e-08!18;CL:0002546!7.08e-08!18;CL:0000076!3.55e-07!62
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004111!5.39e-29!241;UBERON:0000025!2.91e-26!194;UBERON:0000119!2.19e-25!312;UBERON:0000483!2.96e-25!309;UBERON:0000477!1.31e-23!286;UBERON:0000468!2.98e-22!659;UBERON:0000475!1.33e-19!365;UBERON:0000467!2.50e-19!625;UBERON:0000480!5.65e-19!626;UBERON:0002049!8.47e-17!79;UBERON:0007798!8.47e-17!79;UBERON:0000055!1.33e-16!69;UBERON:0001017!3.29e-15!82;UBERON:0003914!3.72e-15!118;UBERON:0004872!7.54e-15!84;UBERON:0005743!8.73e-15!86;UBERON:0001981!3.94e-14!60;UBERON:0007500!3.94e-14!60;UBERON:0004537!3.94e-14!60;UBERON:0006965!3.94e-14!60;UBERON:0000073!1.04e-12!94;UBERON:0001016!1.04e-12!94;UBERON:0001009!1.58e-12!113;UBERON:0000955!3.46e-12!69;UBERON:0006238!3.46e-12!69;UBERON:0001049!9.66e-12!57;UBERON:0005068!9.66e-12!57;UBERON:0006241!9.66e-12!57;UBERON:0007135!9.66e-12!57;UBERON:0004535!1.10e-11!110;UBERON:0002616!1.66e-11!59;UBERON:0000064!3.24e-11!219;UBERON:0000922!5.49e-11!612;UBERON:0004121!6.91e-11!169;UBERON:0000481!8.65e-11!347;UBERON:0002050!1.45e-10!605;UBERON:0005423!1.45e-10!605;UBERON:0000923!2.20e-10!604;UBERON:0005291!2.20e-10!604;UBERON:0006598!2.20e-10!604;UBERON:0002532!2.20e-10!604;UBERON:0007023!2.92e-10!115;UBERON:0000924!3.68e-10!173;UBERON:0006601!3.68e-10!173;UBERON:0003075!7.39e-10!86;UBERON:0007284!7.39e-10!86;UBERON:0001893!1.34e-09!34;UBERON:0003080!1.77e-09!42;UBERON:0000490!2.29e-09!138;UBERON:0002791!3.64e-09!33;UBERON:0002780!4.04e-09!41;UBERON:0001890!4.04e-09!41;UBERON:0006240!4.04e-09!41;UBERON:0002020!4.49e-09!34;UBERON:0003528!4.49e-09!34;UBERON:0001637!4.64e-09!42;UBERON:0003509!4.64e-09!42;UBERON:0004572!4.64e-09!42;UBERON:0001869!5.83e-09!32;UBERON:0002346!7.64e-09!90;UBERON:0000956!3.05e-08!25;UBERON:0000203!3.05e-08!25;UBERON:0001986!7.08e-08!18;UBERON:0004638!7.08e-08!18;UBERON:0004852!7.08e-08!18;UBERON:0000033!7.70e-08!123;UBERON:0002100!9.97e-08!216;UBERON:0000153!2.55e-07!129;UBERON:0007811!2.55e-07!129;UBERON:0002619!4.52e-07!22;UBERON:0001950!4.60e-07!20;UBERON:0000487!5.56e-07!22
}}

Latest revision as of 12:21, 17 September 2013


Full id: C3226_Endothelial_hepatic_Renal_Urothelial_Ewing_Preadipocyte_Fibroblast



Phase1 CAGE Peaks

Hg19::chr12:106532657..106532694,-p2@NUAK1
Hg19::chr12:106532697..106532718,-p4@NUAK1
Hg19::chr12:106532724..106532740,-p1@NUAK1


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><br>

Uber Anatomy
Ontology termp-valuen
anatomical conduit1.77e-27240
tube1.35e-25192
anatomical cluster2.06e-24373
cell layer1.13e-22309
epithelium1.44e-22306
multi-cellular organism1.34e-21656
anatomical system5.26e-18624
anatomical group1.12e-17625
vessel3.48e-1568
central nervous system4.16e-1581
vasculature7.14e-1578
vascular system7.14e-1578
epithelial tube8.31e-15117
splanchnic layer of lateral plate mesoderm4.72e-1383
epithelial tube open at both ends7.10e-1359
blood vessel7.10e-1359
blood vasculature7.10e-1359
vascular cord7.10e-1359
nervous system1.09e-1289
multi-tissue structure1.34e-12342
brain6.39e-1268
future brain6.39e-1268
neural tube1.21e-1156
neural rod1.21e-1156
future spinal cord1.21e-1156
neural keel1.21e-1156
embryo6.77e-11592
developing anatomical structure6.88e-11581
circulatory system8.46e-11112
regional part of nervous system1.06e-1053
regional part of brain1.06e-1053
organ part1.38e-10218
embryonic structure4.56e-10564
cardiovascular system6.29e-10109
telencephalon9.37e-1034
regional part of forebrain1.58e-0941
forebrain1.58e-0941
anterior neural tube1.58e-0941
future forebrain1.58e-0941
germ layer1.66e-09560
germ layer / neural crest1.66e-09560
embryonic tissue1.66e-09560
presumptive structure1.66e-09560
germ layer / neural crest derived structure1.66e-09560
epiblast (generic)1.66e-09560
adult organism1.74e-09114
brain grey matter3.02e-0934
gray matter3.02e-0934
structure with developmental contribution from neural crest3.52e-09132
cerebral hemisphere4.94e-0932
regional part of telencephalon5.61e-0932
ectoderm-derived structure5.85e-09171
ectoderm5.85e-09171
presumptive ectoderm5.85e-09171
ecto-epithelium6.47e-09104
neural plate7.22e-0982
presumptive neural plate7.22e-0982
artery2.19e-0842
arterial blood vessel2.19e-0842
arterial system2.19e-0842
cerebral cortex2.74e-0825
pallium2.74e-0825
organ system subdivision4.21e-08223
neurectoderm8.00e-0886
trunk1.30e-07199
unilaminar epithelium2.22e-07148
blood vessel endothelium2.94e-0718
endothelium2.94e-0718
cardiovascular system endothelium2.94e-0718
regional part of cerebral cortex4.42e-0722
neocortex5.20e-0720


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0057.17.64787
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.18.0808
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.14.67142
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
MA0105.11.5295
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.27.95144
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.07067
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.14.15415
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.222.0921
MA0102.21.88331
MA0258.12.22591
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
CHD2#1106310.34402283411690.0009033701102746880.00658710262842827
E2F1#186934.907389214879320.008460985347239390.0323909258707648



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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