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{{Coexpression_clusters
{
|full_id=C789_retina_Retinal_medulla_stomach_lung_eye_corpus
 

Latest revision as of 11:31, 17 September 2013


Full id: C789_retina_Retinal_medulla_stomach_lung_eye_corpus



Phase1 CAGE Peaks

Hg19::chr11:109990513..109990520,-p@chr11:109990513..109990520
-
Hg19::chr11:61522820..61522823,+p9@C11orf9
Hg19::chr11:61522844..61522875,+p2@C11orf9
Hg19::chr13:99135322..99135327,-p@chr13:99135322..99135327
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Hg19::chr14:87636652..87636657,-p@chr14:87636652..87636657
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Hg19::chr21:36041264..36041274,+p3@CLIC6
Hg19::chr21:36041275..36041282,+p5@CLIC6
Hg19::chr21:36041286..36041333,+p1@CLIC6
Hg19::chr5:70308745..70308754,-p@chr5:70308745..70308754
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Hg19::chr9:140088882..140088898,-p@chr9:140088882..140088898
-


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:0005247voltage-gated chloride channel activity0.0445095728958841
GO:0022844voltage-gated anion channel activity0.0445095728958841
GO:0043168anion binding0.0445095728958841
GO:0031404chloride ion binding0.0445095728958841
GO:0005254chloride channel activity0.0445095728958841
GO:0006821chloride transport0.0445095728958841
GO:0005253anion channel activity0.0445095728958841



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
retinal pigment epithelial cell8.77e-273
visual pigment cell3.00e-204
pigment cell4.09e-1014
Uber Anatomy
Ontology termp-valuen
neural plate5.02e-3382
presumptive neural plate5.02e-3382
neurectoderm2.30e-3186
pigmented layer of retina8.77e-273
presumptive retinal pigmented epithelium8.77e-273
neural tube7.91e-2656
neural rod7.91e-2656
future spinal cord7.91e-2656
neural keel7.91e-2656
ecto-epithelium1.90e-25104
retina1.73e-236
photoreceptor array1.73e-236
posterior segment of eyeball1.73e-236
regional part of nervous system1.76e-2353
regional part of brain1.76e-2353
brainstem7.54e-236
adult organism2.05e-20114
pre-chordal neural plate2.33e-2061
layer of retina3.00e-204
central nervous system1.08e-1981
structure with developmental contribution from neural crest2.03e-19132
brain1.30e-1768
future brain1.30e-1768
telencephalon1.61e-1734
nervous system1.64e-1789
ectoderm-derived structure7.46e-16171
ectoderm7.46e-16171
presumptive ectoderm7.46e-16171
regional part of forebrain2.16e-1441
forebrain2.16e-1441
anterior neural tube2.16e-1441
future forebrain2.16e-1441
posterior neural tube5.80e-1415
chordal neural plate5.80e-1415
brain grey matter7.98e-1434
gray matter7.98e-1434
medulla oblongata2.03e-123
myelencephalon2.03e-123
future myelencephalon2.03e-123
regional part of cerebral cortex3.47e-1222
pons3.57e-123
segmental subdivision of hindbrain1.55e-1112
hindbrain1.55e-1112
presumptive hindbrain1.55e-1112
regional part of telencephalon2.89e-1132
cerebral hemisphere2.94e-1132
cerebral cortex9.90e-1125
pallium9.90e-1125
segmental subdivision of nervous system1.16e-1013
eye3.26e-1021
visual system3.26e-1021
corpus callosum6.31e-101
central nervous system cell part cluster6.31e-101
axon tract6.31e-101
intercerebral commissure6.31e-101
dorsal telencephalic commissure6.31e-101
brain white matter6.31e-101
brain commissure6.31e-101
white matter6.31e-101
nervous system commissure6.31e-101
cerebral hemisphere white matter6.31e-101
pulmonary valve8.91e-101
semi-lunar valve8.91e-101
epididymis1.25e-091
substantia nigra1.36e-091
midbrain nucleus1.36e-091
regional part of midbrain1.36e-091
midbrain1.36e-091
presumptive midbrain1.36e-091
midbrain neural tube1.36e-091
paracentral gyrus1.48e-091
neocortex1.83e-0920
occipital pole1.91e-091
pole of cerebral hemisphere1.91e-091
insula2.67e-091
sense organ6.54e-0924
sensory system6.54e-0924
entire sense organ system6.54e-0924
tube4.04e-08192
organ part5.24e-08218
pigment epithelium of eye1.09e-0711
epithelium1.77e-07306
cell layer2.26e-07309
camera-type eye3.73e-0720
simple eye3.73e-0720
immature eye3.73e-0720
ocular region3.73e-0720
eyeball of camera-type eye3.73e-0720
optic cup3.73e-0720
optic vesicle3.73e-0720
eye primordium3.73e-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)
MA0003.10.456919
MA0004.10.380329
MA0006.10.236135
MA0007.11.69684
MA0009.10.828613
MA0014.10.0679667
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.11.71387
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.965046
MA0051.10.473017
MA0052.10.753928
MA0055.10.014035
MA0056.10
MA0057.11.22133
MA0058.10.293055
MA0059.10.291897
MA0060.10.848451
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.11.05557
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.14.77354
MA0074.11.19015
MA0076.10.307383
MA0077.10.790956
MA0078.11.39444
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.646502
MA0105.10.189717
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.353333
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.945459
MA0146.10.243477
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.138005
MA0138.22.38893
MA0002.20.407187
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.22.25856
MA0065.20.0371828
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.11.58042
MA0155.10.545933
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.10.715303
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.117453
MA0102.21.36707
MA0258.10.919347
MA0259.10.191914
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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