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Coexpression cluster:C2100: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2100_epithelioid_Mesenchymal_Adipocyte_tenocyte_Smooth_Chondrocyte_Olfactory
|id=C2100
}}

Latest revision as of 11:58, 17 September 2013


Full id: C2100_epithelioid_Mesenchymal_Adipocyte_tenocyte_Smooth_Chondrocyte_Olfactory



Phase1 CAGE Peaks

Hg19::chr11:119289379..119289398,-p7@THY1
Hg19::chr11:119289504..119289517,-p5@THY1
Hg19::chr11:119293872..119293897,-p1@THY1
Hg19::chr11:119293903..119293917,-p2@THY1


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
structure with developmental contribution from neural crest1.78e-20132
central nervous system2.26e-1881
neural tube1.04e-1756
neural rod1.04e-1756
future spinal cord1.04e-1756
neural keel1.04e-1756
ectoderm-derived structure1.38e-17171
ectoderm1.38e-17171
presumptive ectoderm1.38e-17171
regional part of nervous system2.14e-1753
regional part of brain2.14e-1753
nervous system2.47e-1789
brain1.25e-1668
future brain1.25e-1668
neural plate2.14e-1682
presumptive neural plate2.14e-1682
neurectoderm2.74e-1686
ecto-epithelium1.31e-14104
regional part of forebrain1.53e-1441
forebrain1.53e-1441
anterior neural tube1.53e-1441
future forebrain1.53e-1441
cerebral hemisphere2.38e-1432
multi-tissue structure3.75e-14342
brain grey matter4.88e-1434
gray matter4.88e-1434
telencephalon6.01e-1434
regional part of telencephalon2.43e-1332
dense mesenchyme tissue5.07e-1373
pre-chordal neural plate8.05e-1361
paraxial mesoderm9.62e-1372
presumptive paraxial mesoderm9.62e-1372
somite2.14e-1271
presomitic mesoderm2.14e-1271
presumptive segmental plate2.14e-1271
dermomyotome2.14e-1271
trunk paraxial mesoderm2.14e-1271
epithelial vesicle5.18e-1278
cerebral cortex1.33e-1125
pallium1.33e-1125
regional part of cerebral cortex3.52e-1122
epithelium4.02e-11306
cell layer5.62e-11309
multilaminar epithelium1.75e-1083
multi-cellular organism3.00e-10656
neocortex3.02e-1020
skeletal muscle tissue6.96e-1062
striated muscle tissue6.96e-1062
myotome6.96e-1062
muscle tissue8.97e-1064
musculature8.97e-1064
musculature of body8.97e-1064
anatomical cluster1.53e-09373
integument2.47e-0946
integumental system2.47e-0946
surface structure3.15e-0999
tube8.84e-09192
trunk mesenchyme1.71e-08122
anatomical conduit1.85e-08240
adult organism4.70e-08114
organ part1.12e-07218
adipose tissue1.51e-0714
mesenchyme2.42e-07160
entire embryonic mesenchyme2.42e-07160
skin of body3.52e-0741
organ system subdivision5.15e-07223
anatomical system9.38e-07624


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.16.9203
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.12.01886
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.12.05499
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.11.813
MA0062.20.931615
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.72671
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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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