Personal tools

Coexpression cluster:C494

From FANTOM5_SSTAR

Revision as of 05:15, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


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)

{{{tfbs_overrepresentation_jaspar}}}



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.