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{{Coexpression_clusters
{
|full_id=C494_occipital_medial_brain_Whole_caudate_parietal_blood
|gostat_on_coexpression_clusters

Latest revision as of 11:24, 17 September 2013


Full id: C494_occipital_medial_brain_Whole_caudate_parietal_blood



Phase1 CAGE Peaks

Hg19::chr11:124615395..124615405,+p@chr11:124615395..124615405
+
Hg19::chr11:124615417..124615426,+p@chr11:124615417..124615426
+
Hg19::chr11:124615444..124615454,+p@chr11:124615444..124615454
+
Hg19::chr11:124615466..124615503,+p@chr11:124615466..124615503
+
Hg19::chr11:124615584..124615600,+p@chr11:124615584..124615600
+
Hg19::chr11:124616294..124616374,+p@chr11:124616294..124616374
+
Hg19::chr11:124616375..124616422,+p@chr11:124616375..124616422
+
Hg19::chr11:124616427..124616476,+p@chr11:124616427..124616476
+
Hg19::chr11:124616482..124616540,+p@chr11:124616482..124616540
+
Hg19::chr11:124616552..124616569,+p@chr11:124616552..124616569
+
Hg19::chr11:124616611..124616623,+p@chr11:124616611..124616623
+
Hg19::chr11:124616640..124616647,+p@chr11:124616640..124616647
+
Hg19::chr11:124616709..124616718,+p@chr11:124616709..124616718
+
Hg19::chr11:35275624..35275635,-p14@SLC1A2
Hg19::chr11:35277083..35277090,-p47@SLC1A2
Hg19::chr12:49389153..49389154,-p@chr12:49389153..49389154
-
Hg19::chr16:743961..743974,-p@chr16:743961..743974
-
Hg19::chr2:68479697..68479708,-p2@PPP3R1
Hg19::chr8:21939098..21939104,+p@chr8:21939098..21939104
+


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

p.valueFDRnGenesnPathwayName
1.93288158883898e-050.006117570228675372126Glutamatergic synapse (KEGG):04724
3.38223597386681e-060.00214095537145769253Amyotrophic lateral sclerosis (ALS) (KEGG):05014



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:0005517calmodulin inhibitor activity0.00382662447319203
GO:0004723calcium-dependent protein serine/threonine phosphatase activity0.00382662447319203
GO:0005955calcineurin complex0.0051020157702358
GO:0005313L-glutamate transmembrane transporter activity0.00650382537410799
GO:0015172acidic amino acid transmembrane transporter activity0.00650382537410799
GO:0015813L-glutamate transport0.00650382537410799
GO:0015800acidic amino acid transport0.00650382537410799
GO:0017153sodium:dicarboxylate symporter activity0.00650382537410799
GO:0005310dicarboxylic acid transmembrane transporter activity0.00650382537410799
GO:0006835dicarboxylic acid transport0.00650382537410799
GO:0015179L-amino acid transmembrane transporter activity0.0111270830268056
GO:0005343organic acid:sodium symporter activity0.011473621593484
GO:0015296anion:cation symporter activity0.011473621593484
GO:0008287protein serine/threonine phosphatase complex0.0155312468165728
GO:0015171amino acid transmembrane transporter activity0.0155312468165728
GO:0004722protein serine/threonine phosphatase activity0.0155312468165728
GO:0006865amino acid transport0.0157409186351371
GO:0015837amine transport0.0164476067567351
GO:0015370solute:sodium symporter activity0.0164476067567351
GO:0046943carboxylic acid transmembrane transporter activity0.0164476067567351
GO:0046942carboxylic acid transport0.0164476067567351
GO:0015849organic acid transport0.0164476067567351
GO:0005342organic acid transmembrane transporter activity0.0164476067567351
GO:0015294solute:cation symporter activity0.018146502540626
GO:0005516calmodulin binding0.0215380072397654
GO:0008509anion transmembrane transporter activity0.0306664547475256
GO:0015293symporter activity0.0341767369167349
GO:0007268synaptic transmission0.0394648935897162
GO:0004721phosphoprotein phosphatase activity0.0411120977212879
GO:0019226transmission of nerve impulse0.0418896566957398
GO:0015291secondary active transmembrane transporter activity0.0442040623661732



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
telencephalon1.56e-6234
cerebral hemisphere2.84e-6232
regional part of forebrain8.35e-5941
forebrain8.35e-5941
anterior neural tube8.35e-5941
future forebrain8.35e-5941
brain grey matter6.81e-5834
gray matter6.81e-5834
regional part of telencephalon1.84e-5732
regional part of nervous system3.96e-5053
regional part of brain3.96e-5053
regional part of cerebral cortex5.13e-5022
neural tube5.14e-4756
neural rod5.14e-4756
future spinal cord5.14e-4756
neural keel5.14e-4756
neocortex1.07e-4420
adult organism7.26e-44114
cerebral cortex1.39e-4325
pallium1.39e-4325
brain2.95e-4268
future brain2.95e-4268
central nervous system7.62e-3981
pre-chordal neural plate4.36e-3761
nervous system4.44e-3489
neurectoderm1.19e-2986
neural plate1.70e-2982
presumptive neural plate1.70e-2982
ecto-epithelium4.81e-23104
basal ganglion1.80e-209
nuclear complex of neuraxis1.80e-209
aggregate regional part of brain1.80e-209
collection of basal ganglia1.80e-209
cerebral subcortex1.80e-209
blood7.66e-1915
haemolymphatic fluid7.66e-1915
organism substance7.66e-1915
gyrus8.66e-196
structure with developmental contribution from neural crest1.15e-17132
temporal lobe1.36e-156
ectoderm-derived structure1.54e-15171
ectoderm1.54e-15171
presumptive ectoderm1.54e-15171
neural nucleus1.98e-159
nucleus of brain1.98e-159
telencephalic nucleus3.49e-157
limbic system4.10e-155
corpus striatum6.90e-134
striatum6.90e-134
ventral part of telencephalon6.90e-134
future corpus striatum6.90e-134
organ system subdivision2.45e-11223
occipital lobe8.79e-115
parietal lobe1.43e-105
frontal cortex3.57e-103
caudate-putamen3.80e-103
dorsal striatum3.80e-103
tube1.84e-09192
middle temporal gyrus1.97e-072
middle frontal gyrus2.23e-072
caudate nucleus2.30e-072
future caudate nucleus2.30e-072
germ layer2.73e-07560
germ layer / neural crest2.73e-07560
embryonic tissue2.73e-07560
presumptive structure2.73e-07560
germ layer / neural crest derived structure2.73e-07560
epiblast (generic)2.73e-07560
embryonic structure3.87e-07564
amygdala4.52e-072
Ammon's horn5.76e-072
lobe parts of cerebral cortex5.76e-072
hippocampal formation5.76e-072
limbic lobe5.76e-072
meninx6.89e-072
membrane organ6.89e-072
meningeal cluster6.89e-072
hematopoietic system8.02e-0798
blood island8.02e-0798


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)
MA0003.11.42762
MA0004.10.193314
MA0006.10.308609
MA0007.10.532323
MA0009.10.580032
MA0014.10.096993
MA0017.10.114723
MA0019.10.824541
MA0024.12.11236
MA0025.10.70396
MA0027.12.15732
MA0028.11.65705
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.10.269828
MA0040.10.507819
MA0041.10.206566
MA0042.10.183918
MA0043.10.580321
MA0046.10.570066
MA0048.10.0472517
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.0183725
MA0056.10
MA0057.10.441948
MA0058.10.12994
MA0059.10.805771
MA0060.10.0387582
MA0061.10.535933
MA0063.10
MA0066.15.8109
MA0067.10.879057
MA0068.10.0841176
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.10.552241
MA0073.11.63857
MA0074.10.734236
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.80621
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.11.45418
MA0089.10
MA0090.10.455738
MA0091.10.195166
MA0092.10.168981
MA0093.10.0941737
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.317957
MA0103.10.295078
MA0105.10.611869
MA0106.10.302526
MA0107.10.0591705
MA0108.20.432749
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.10.207884
MA0115.10.805883
MA0116.10.477333
MA0117.10.614633
MA0119.10.119385
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.755761
MA0139.10.264531
MA0140.10.238066
MA0141.10.128074
MA0142.10.407878
MA0143.10.315941
MA0144.10.0508083
MA0145.10.675341
MA0146.10.0164781
MA0147.10.485912
MA0148.10.211171
MA0149.10.230803
MA0062.20.826291
MA0035.20.237534
MA0039.21.8612
MA0138.20.347473
MA0002.20.0346057
MA0137.20.105044
MA0104.20.34888
MA0047.20.292798
MA0112.20.136364
MA0065.20.468021
MA0150.10.145358
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.10.38017
MA0155.10.392871
MA0156.10.106343
MA0157.10.384449
MA0158.10
MA0159.16.66403
MA0160.10.222325
MA0161.10
MA0162.10.776421
MA0163.10.933861
MA0164.10.32594
MA0080.21.07751
MA0018.20.30364
MA0099.20.243305
MA0079.21.03584
MA0102.21.09681
MA0258.10.399676
MA0259.10.235101
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
CTBP2#14881342.91163181111921.04100712274376e-192.58246420171582e-17
CTCF#1066492.53906880829870.004103170101193370.0195908833408857
JUND#372772.576981452268270.01265915680641840.0457619908520136
RAD21#588573.81501248779970.001380200329438870.0089844641115848
SMC3#912675.542869995501570.0001411204463540470.00183978008947327
SP1#666782.399318475006690.01079403202759020.0398078290522084
SPI1#668883.454452003588520.001053424630127970.00744425299045502
SUZ12#2351237.913018038588880.0060558071115970.0268595761212927
ZNF143#770274.974007150820810.0002769509842696340.00294967202183727



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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