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Coexpression cluster:C4797: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4797_keratoacanthoma_temporal_cervical_brain_Mammary_occipital_oral
|id=C4797
|ontology_enrichment_celltype=CL:0002321!3.72e-16!248;CL:0000220!4.86e-16!246;CL:0000066!3.10e-11!254;CL:0002076!1.27e-09!43;CL:0000076!8.71e-09!62;CL:0002368!1.81e-07!13;CL:0000055!4.52e-07!180;CL:0000221!7.88e-07!71
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!1.26e-29!365;UBERON:0000119!6.45e-28!312;UBERON:0000483!7.86e-28!309;UBERON:0004111!1.96e-27!241;UBERON:0000481!5.41e-27!347;UBERON:0004121!1.51e-26!169;UBERON:0000477!3.21e-26!286;UBERON:0000924!4.82e-25!173;UBERON:0006601!4.82e-25!173;UBERON:0000033!1.17e-23!123;UBERON:0000153!3.67e-22!129;UBERON:0007811!3.67e-22!129;UBERON:0000468!9.68e-21!659;UBERON:0000922!2.47e-20!612;UBERON:0000025!6.20e-20!194;UBERON:0000480!1.14e-19!626;UBERON:0000467!2.00e-19!625;UBERON:0002050!4.34e-19!605;UBERON:0005423!4.34e-19!605;UBERON:0000923!1.10e-18!604;UBERON:0005291!1.10e-18!604;UBERON:0006598!1.10e-18!604;UBERON:0002532!1.10e-18!604;UBERON:0003075!2.90e-18!86;UBERON:0007284!2.90e-18!86;UBERON:0001017!3.49e-18!82;UBERON:0000064!4.12e-18!219;UBERON:0001049!6.37e-18!57;UBERON:0005068!6.37e-18!57;UBERON:0006241!6.37e-18!57;UBERON:0007135!6.37e-18!57;UBERON:0005743!4.09e-17!86;UBERON:0000073!1.26e-16!94;UBERON:0001016!1.26e-16!94;UBERON:0002346!1.77e-16!90;UBERON:0001869!5.02e-16!32;UBERON:0000955!7.35e-16!69;UBERON:0006238!7.35e-16!69;UBERON:0002616!7.63e-16!59;UBERON:0002020!9.62e-16!34;UBERON:0003528!9.62e-16!34;UBERON:0003080!1.64e-15!42;UBERON:0001893!2.10e-15!34;UBERON:0002780!4.46e-15!41;UBERON:0001890!4.46e-15!41;UBERON:0006240!4.46e-15!41;UBERON:0002791!6.87e-15!33;UBERON:0003056!8.21e-15!61;UBERON:0002619!1.91e-13!22;UBERON:0000956!4.45e-13!25;UBERON:0000203!4.45e-13!25;UBERON:0001950!1.68e-12!20;UBERON:0000062!4.77e-11!511;UBERON:0007023!1.47e-10!115;UBERON:0004119!9.49e-09!169;UBERON:0000925!9.49e-09!169;UBERON:0006595!9.49e-09!169;UBERON:0000464!2.20e-08!104;UBERON:0001004!4.42e-08!72;UBERON:0000161!5.26e-08!35;UBERON:0001444!5.39e-08!48;UBERON:0000165!8.78e-08!28;UBERON:0000930!8.78e-08!28;UBERON:0003102!1.22e-07!95;UBERON:0002100!2.13e-07!216;UBERON:0000166!2.47e-07!21;UBERON:0003104!3.13e-07!238;UBERON:0009142!3.13e-07!238;UBERON:0001007!9.74e-07!155;UBERON:0001555!9.74e-07!155;UBERON:0007026!9.74e-07!155
}}

Latest revision as of 14:19, 17 September 2013


Full id: C4797_keratoacanthoma_temporal_cervical_brain_Mammary_occipital_oral



Phase1 CAGE Peaks

Hg19::chr9:124461400..124461433,+p2@DAB2IP
Hg19::chr9:124461438..124461472,+p5@DAB2IP
Hg19::chr9:124461473..124461505,+p3@DAB2IP


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>

Cell Type
Ontology termp-valuen
embryonic cell1.21e-16250
epithelial cell9.78e-12253
endo-epithelial cell3.56e-1042
squamous epithelial cell2.29e-0863
ectodermal cell2.88e-0772
ecto-epithelial cell3.35e-0734
respiratory epithelial cell3.43e-0713
Uber Anatomy
Ontology termp-valuen
anatomical cluster3.91e-31373
cell layer1.95e-26309
epithelium3.63e-26306
multi-tissue structure2.24e-25342
ectoderm-derived structure3.64e-24171
ectoderm3.64e-24171
presumptive ectoderm3.64e-24171
anatomical conduit4.31e-24240
multi-cellular organism4.38e-22656
anatomical group5.51e-21625
anatomical system8.13e-21624
ecto-epithelium1.30e-20104
structure with developmental contribution from neural crest5.85e-19132
embryo6.76e-19592
organ part1.19e-17218
tube1.66e-17192
organ system subdivision2.00e-17223
central nervous system4.55e-1781
neural plate7.06e-1782
presumptive neural plate7.06e-1782
nervous system7.86e-1789
neural tube1.90e-1656
neural rod1.90e-1656
future spinal cord1.90e-1656
neural keel1.90e-1656
developing anatomical structure2.52e-16581
embryonic structure5.35e-16564
regional part of nervous system1.12e-1553
regional part of brain1.12e-1553
germ layer3.71e-15560
germ layer / neural crest3.71e-15560
embryonic tissue3.71e-15560
presumptive structure3.71e-15560
germ layer / neural crest derived structure3.71e-15560
epiblast (generic)3.71e-15560
brain5.89e-1568
future brain5.89e-1568
neurectoderm9.35e-1586
cerebral hemisphere2.78e-1432
brain grey matter4.61e-1434
gray matter4.61e-1434
telencephalon8.88e-1434
regional part of telencephalon1.71e-1332
regional part of forebrain2.09e-1341
forebrain2.09e-1341
anterior neural tube2.09e-1341
future forebrain2.09e-1341
pre-chordal neural plate2.46e-1361
organism subdivision2.13e-12264
regional part of cerebral cortex4.67e-1222
cerebral cortex1.77e-1125
pallium1.77e-1125
neocortex2.15e-1120
organ2.32e-11503
adult organism3.39e-09114
surface structure4.68e-0899
head5.69e-0856
endoderm-derived structure1.01e-07160
endoderm1.01e-07160
presumptive endoderm1.01e-07160
subdivision of head1.02e-0749
orifice1.49e-0736
anatomical space1.52e-0795
respiratory system2.53e-0774
mouth3.36e-0729
stomodeum3.36e-0729
anterior region of body9.21e-0762
craniocervical region9.21e-0762


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
MA0014.13.90467
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
MA0056.10
MA0057.12.4146
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
MA0073.14.54482
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
MA0105.11.5295
MA0106.10.986396
MA0107.11.36919
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
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.27.10722
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.22.88736
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.12.30945
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.211.5899
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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

No analysis results for this cluster

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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