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Coexpression cluster:C2678: Difference between revisions

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{{Coexpression_clusters
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O:0001635!calcitonin gene-related polypeptide receptor activity!0.00276698457553279!10203$GO:0004948!calcitonin receptor activity!0.00553372479694806!10203$GO:0048661!positive regulation of smooth muscle cell proliferation!0.00737786532194403!10203$GO:0048660!regulation of smooth muscle cell proliferation!0.00774607439651214!10203$GO:0048659!smooth muscle cell proliferation!0.00774607439651214!10203$GO:0033002!muscle cell proliferation!0.00922070262497986!10203$GO:0007189!G-protein signaling, adenylate cyclase activating pathway!0.0138269813688443!10203$GO:0001633!secretin-like receptor activity!0.0138269813688443!10203$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.023612775104622!10203$GO:0019933!cAMP-mediated signaling!0.023612775104622!10203$GO:0007507!heart development!0.023612775104622!10203$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0259208404334235!10203$GO:0019935!cyclic-nucleotide-mediated signaling!0.0259208404334235!10203$GO:0005886!plasma membrane!0.0423490121090567!51705;10203$GO:0008284!positive regulation of cell proliferation!0.0428337292268629!10203$GO:0019932!second-messenger-mediated 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|full_id=C2678_lung_Endothelial_Lymphatic_mature_migratory_adipose_Mast
|id=C2678
}}

Latest revision as of 12:10, 17 September 2013


Full id: C2678_lung_Endothelial_Lymphatic_mature_migratory_adipose_Mast



Phase1 CAGE Peaks

Hg19::chr2:188312865..188312876,-p3@CALCRL
Hg19::chr2:188312971..188312987,-p1@CALCRL
Hg19::chr2:188312993..188313033,-p2@CALCRL
Hg19::chr4:101439242..101439256,-p5@EMCN


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

GO IDGO nameFDR corrected p-value
GO:0001635calcitonin gene-related polypeptide receptor activity0.00276698457553279
GO:0004948calcitonin receptor activity0.00553372479694806
GO:0048661positive regulation of smooth muscle cell proliferation0.00737786532194403
GO:0048660regulation of smooth muscle cell proliferation0.00774607439651214
GO:0048659smooth muscle cell proliferation0.00774607439651214
GO:0033002muscle cell proliferation0.00922070262497986
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0138269813688443
GO:0001633secretin-like receptor activity0.0138269813688443
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.023612775104622
GO:0019933cAMP-mediated signaling0.023612775104622
GO:0007507heart development0.023612775104622
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0259208404334235
GO:0019935cyclic-nucleotide-mediated signaling0.0259208404334235
GO:0005886plasma membrane0.0423490121090567
GO:0008284positive regulation of cell proliferation0.0428337292268629
GO:0019932second-messenger-mediated signaling0.0461648561898207



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
adult organism4.84e-31114
embryonic structure6.82e-17564
germ layer1.41e-16560
germ layer / neural crest1.41e-16560
embryonic tissue1.41e-16560
presumptive structure1.41e-16560
germ layer / neural crest derived structure1.41e-16560
epiblast (generic)1.41e-16560
anatomical conduit3.62e-16240
multi-cellular organism4.72e-16656
developing anatomical structure1.12e-15581
tube1.27e-15192
embryo2.57e-15592
neural tube3.32e-1556
neural rod3.32e-1556
future spinal cord3.32e-1556
neural keel3.32e-1556
circulatory system6.90e-14112
anatomical system9.33e-14624
regional part of nervous system1.59e-1353
regional part of brain1.59e-1353
anatomical group1.99e-13625
lateral plate mesoderm2.05e-13203
central nervous system2.34e-1381
cardiovascular system4.21e-13109
vasculature1.22e-1278
vascular system1.22e-1278
structure with developmental contribution from neural crest1.22e-12132
mesoderm1.24e-12315
mesoderm-derived structure1.24e-12315
presumptive mesoderm1.24e-12315
splanchnic layer of lateral plate mesoderm2.94e-1283
brain4.11e-1268
future brain4.11e-1268
anatomical cluster4.53e-12373
vessel5.06e-1268
blood vessel endothelium1.11e-1118
endothelium1.11e-1118
cardiovascular system endothelium1.11e-1118
neurectoderm1.47e-1186
nervous system1.80e-1189
neural plate4.84e-1182
presumptive neural plate4.84e-1182
tissue5.92e-11773
epithelial tube open at both ends2.90e-1059
blood vessel2.90e-1059
blood vasculature2.90e-1059
vascular cord2.90e-1059
regional part of forebrain3.92e-1041
forebrain3.92e-1041
anterior neural tube3.92e-1041
future forebrain3.92e-1041
simple squamous epithelium4.46e-0922
brain grey matter1.12e-0834
gray matter1.12e-0834
cell layer1.29e-08309
telencephalon2.35e-0834
epithelium3.21e-08306
squamous epithelium7.33e-0825
regional part of telencephalon7.52e-0832
cerebral hemisphere9.44e-0832
ecto-epithelium6.51e-07104
primary circulatory organ6.65e-0727
regional part of cerebral cortex7.70e-0722
immune system9.10e-0793


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.12.98182
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
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
MA0143.12.05538
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0021048
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235336.74846648167080.005032452776317940.0234730175296266
GATA2#2624412.7449317335543.78864877853583e-050.000722576131814288
JUN#372539.384621894252250.001918994502030470.0112873319890494
RAD21#588537.766275421592250.0033411193858720.0172701394477152
SETDB1#9869330.24001963350795.98509618524166e-050.000985149661923489
SMC3#9126311.28369963369960.001115802366868050.00765759517632624
TRIM28#10155313.94289378394690.0005972858184258420.00499479010253635
WRNIP1#56897382.36497326203212.99417904077464e-060.00010146303206991



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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