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Coexpression cluster:C751: Difference between revisions

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{{Coexpression_clusters
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0115.1;1.02805,MA0116.1;0.159642,MA0117.1;0.827487,MA0119.1;0.250314,MA0122.1;0.852927,MA0124.1;0.98702,MA0125.1;0.904129,MA0130.1;0,MA0131.1;0.550695,MA0132.1;0,MA0133.1;0,MA0135.1;0.820382,MA0136.1;0.450422,MA0139.1;0.307853,MA0140.1;0.405425,MA0141.1;1.33697,MA0142.1;0.602852,MA0143.1;1.24556,MA0144.1;1.39025,MA0145.1;0.277793,MA0146.1;1.56298,MA0147.1;1.51125,MA0148.1;0.372124,MA0149.1;0.396509,MA0062.2;0.0969238,MA0035.2;0.404774,MA0039.2;0.964131,MA0138.2;0.534556,MA0002.2;0.725804,MA0137.2;0.649788,MA0104.2;2.45237,MA0047.2;0.47109,MA0112.2;0.106997,MA0065.2;0.0286783,MA0150.1;0.286461,MA0151.1;0,MA0152.1;0.411494,MA0153.1;0.887528,MA0154.1;0.989789,MA0155.1;0.245306,MA0156.1;0.231442,MA0157.1;0.576556,MA0158.1;0,MA0159.1;0.162854,MA0160.1;0.386031,MA0161.1;0,MA0162.1;4.65706,MA0163.1;6.26956,MA0164.1;0.509774,MA0080.2;0.21336,MA0018.2;0.483823,MA0099.2;0.411824,MA0079.2;10.9787,MA0102.2;1.32663,MA0258.1;0.135061,MA0259.1;0.504687,MA0442.1;0}}
|full_id=C751_heart_pineal_left_cerebellum_pons_putamen_Mesothelial
|id=C751
}}

Latest revision as of 11:30, 17 September 2013


Full id: C751_heart_pineal_left_cerebellum_pons_putamen_Mesothelial



Phase1 CAGE Peaks

Hg19::chr13:30079614..30079618,+p@chr13:30079614..30079618
+
Hg19::chr16:58497281..58497330,+p6@NDRG4
Hg19::chr16:58497337..58497348,+p9@NDRG4
Hg19::chr16:58497587..58497668,+p2@NDRG4
Hg19::chr16:58498177..58498193,+p4@NDRG4
Hg19::chr16:58498194..58498236,+p3@NDRG4
Hg19::chr1:62417957..62417993,+p4@INADL
Hg19::chr1:62417997..62418034,+p3@INADL
Hg19::chr2:220492344..220492368,+p1@SLC4A3
Hg19::chr2:220492373..220492391,+p2@SLC4A3
Hg19::chr5:31639211..31639288,+p1@PDZD2


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:0005911intercellular junction0.0104492723300696
GO:0030054cell junction0.0261672940711137
GO:0044459plasma membrane part0.0261672940711137
GO:0015106bicarbonate transmembrane transporter activity0.032980560816889
GO:0005452inorganic anion exchanger activity0.032980560816889
GO:0015380anion exchanger activity0.032980560816889
GO:0015301anion:anion antiporter activity0.032980560816889
GO:0015108chloride transmembrane transporter activity0.032980560816889
GO:0005886plasma membrane0.0392005153929385



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.15e-67114
neural tube2.07e-5556
neural rod2.07e-5556
future spinal cord2.07e-5556
neural keel2.07e-5556
regional part of nervous system5.67e-5253
regional part of brain5.67e-5253
neural plate2.59e-5182
presumptive neural plate2.59e-5182
central nervous system2.53e-4981
neurectoderm6.18e-4886
nervous system1.23e-4589
regional part of forebrain1.13e-4341
forebrain1.13e-4341
anterior neural tube1.13e-4341
future forebrain1.13e-4341
brain1.22e-4368
future brain1.22e-4368
ecto-epithelium3.14e-43104
pre-chordal neural plate4.23e-3861
structure with developmental contribution from neural crest5.11e-36132
brain grey matter1.06e-3434
gray matter1.06e-3434
telencephalon1.14e-3434
cerebral hemisphere1.22e-3232
regional part of telencephalon3.70e-3232
ectoderm-derived structure1.61e-29171
ectoderm1.61e-29171
presumptive ectoderm1.61e-29171
regional part of cerebral cortex6.02e-2822
neocortex2.59e-2520
cerebral cortex8.77e-2425
pallium8.77e-2425
organ system subdivision7.00e-20223
anatomical cluster1.45e-17373
tube7.33e-15192
anatomical conduit2.22e-13240
organ1.21e-12503
basal ganglion1.26e-129
nuclear complex of neuraxis1.26e-129
aggregate regional part of brain1.26e-129
collection of basal ganglia1.26e-129
cerebral subcortex1.26e-129
posterior neural tube1.36e-1215
chordal neural plate1.36e-1215
neural nucleus1.80e-129
nucleus of brain1.80e-129
multi-tissue structure1.09e-11342
embryo1.03e-10592
epithelium1.88e-10306
diencephalon2.09e-107
future diencephalon2.09e-107
organ part2.32e-10218
cell layer3.85e-10309
telencephalic nucleus5.76e-107
multi-cellular organism1.15e-09656
segmental subdivision of hindbrain1.66e-0912
hindbrain1.66e-0912
presumptive hindbrain1.66e-0912
brainstem2.46e-096
gyrus2.91e-096
developing anatomical structure8.45e-09581
anatomical system1.28e-08624
segmental subdivision of nervous system1.39e-0813
anatomical group1.50e-08625
limbic system3.18e-085
embryonic structure4.41e-08564
parietal lobe6.78e-085
male reproductive organ7.35e-0811
occipital lobe7.92e-085
temporal lobe1.02e-076
germ layer1.30e-07560
germ layer / neural crest1.30e-07560
embryonic tissue1.30e-07560
presumptive structure1.30e-07560
germ layer / neural crest derived structure1.30e-07560
epiblast (generic)1.30e-07560
corpus striatum6.20e-074
striatum6.20e-074
ventral part of telencephalon6.20e-074
future corpus striatum6.20e-074
gland of diencephalon9.44e-074
neuroendocrine gland9.44e-074
regional part of diencephalon9.86e-074


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)
MA0003.15.13492
MA0004.10.349539
MA0006.11.14056
MA0007.10.332734
MA0009.10.79061
MA0014.18.01823
MA0017.10.682686
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.637069
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.959796
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.11.57917
MA0050.10.338274
MA0051.10.439895
MA0052.11.70446
MA0055.11.04456
MA0056.10
MA0057.11.53339
MA0058.10.732537
MA0059.12.06769
MA0060.10.119532
MA0061.15.20051
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.943943
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.708344
MA0074.10.439193
MA0076.10.278993
MA0077.11.78038
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.11.10483
MA0089.10
MA0090.10.792817
MA0091.10.351901
MA0092.10.318032
MA0093.10.61153
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.11.81378
MA0103.11.11087
MA0105.110.7792
MA0106.10.482519
MA0107.13.61529
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.307853
MA0140.10.405425
MA0141.11.33697
MA0142.10.602852
MA0143.11.24556
MA0144.11.39025
MA0145.10.277793
MA0146.11.56298
MA0147.11.51125
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.964131
MA0138.20.534556
MA0002.20.725804
MA0137.20.649788
MA0104.22.45237
MA0047.20.47109
MA0112.20.106997
MA0065.20.0286783
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.989789
MA0155.10.245306
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.14.65706
MA0163.16.26956
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.210.9787
MA0102.21.32663
MA0258.10.135061
MA0259.10.504687
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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