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Coexpression cluster:C472: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.726922,0.132539,0.348202,0.577617,0.601808,0.574869,0.253108,0.138548,0.31878,0.386207,0.177199,0.286323,0.718946,0.244498,0.285984,0.65729,0.43322,1.23386,0.105136,0.514268,0.707996,0.176757,0.192508,0.280777,0.417677,0.304148,0.194566,0.558352,0.0865304,0.33292,0.489389,0.465029,0.393386,0.0955518,0.0681935,2.78724,0.0667305,0.576802,0.206488,3.22073,0.0675531,0.152186,0.354107,0.283867,0.700168,0.394509,0.253928,0.507207,0.318317,0.292421,0.315441,0.262847,0.403678,0.532773,0.671855,0.246686,1.03902,0.633499,0.332598,0.221865,0.500944,0.710665,0.319823,0.409576,0.269358,0.380605,0.754286,1.10771,1.15512,0.950487,0.442439,0.608338,0.223781,0.670004,0.020227,0.078586,0.178047,1.02338,0.45319,0.130356,0.497004,0.408665,0.269087,0.330114,0.622646,0.0261694,0.173153,0.0595657,0.336397,1.20481,0.84263,0.598,0.4797,0.722259,0.60366,0.439931,0.768521,0.517267,0.340143,0.275452,0.457044,0.474756,0.512318,0.436368,0.371019,0.517502,0.422802,0.241933,0.826645,1.42426,0.736834,0.509866,0.34005,0.183573,0.797061,0.86793,0.159682,0.945065,0.378653,0.0497592,0.662347,0.889041,0.195973,0.761257,0.90249,0.395934,0.248345,0.484077,0.701879,0.054333,0.598629,0.164582,0.715286,0.275188,0.854902,1.88002,1.49034,0.55929,0.814541,1.65405,1.25623,0.779227,0.696623,0.514137,0.372477,2.5594,0.35869,1.49614,0.150069,0.710803,0.0912904,0.0402223,0.598976,0.30216,1.31002,0.980005,0.32333,0.0779979,0.134125,0.37363,0.77808,0.582159,1.14758,0.378488,0.385896,0.268483,0.375051,0.702336,0.114242
}}
}}

Revision as of 14:14, 26 November 2012


Full id: C472_amygdala_medial_hippocampus_insula_frontal_temporal_paracentral



Phase1 CAGE Peaks

Hg19::chr10:103946143..103946171,+p@chr10:103946143..103946171
+
Hg19::chr10:117026289..117026299,+p@chr10:117026289..117026299
+
Hg19::chr11:64059464..64059475,+p5@KCNK4
Hg19::chr11:99941186..99941205,+p5@CNTN5
Hg19::chr14:76241802..76241811,+p@chr14:76241802..76241811
+
Hg19::chr17:74864215..74864221,+p9@MGAT5B
Hg19::chr19:54409564..54409575,+p@chr19:54409564..54409575
+
Hg19::chr19:55690675..55690695,-p5@SYT5
Hg19::chr19:7982540..7982547,+p@chr19:7982540..7982547
+
Hg19::chr20:54579338..54579354,-p3@CBLN4
Hg19::chr21:22881212..22881223,+p@chr21:22881212..22881223
+
Hg19::chr2:242815160..242815176,+p@chr2:242815160..242815176
+
Hg19::chr2:80816155..80816168,+p9@CTNNA2
Hg19::chr5:146257643..146257659,-p19@PPP2R2B
Hg19::chr5:72509751..72509785,+p1@ENST00000513379
p1@ENST00000515556
Hg19::chr6:130742231..130742252,+p15@TMEM200A
Hg19::chr7:130151475..130151483,+p@chr7:130151475..130151483
+
Hg19::chr8:117658838..117658848,-p@chr8:117658838..117658848
-
Hg19::chr9:88058857..88058883,-p@chr9:88058857..88058883
-
Hg19::chrX:12083655..12083665,+p@chrX:12083655..12083665
+


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:0030054cell junction0.00734677943850633
GO:0030144alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity0.022457689244041
GO:0055038recycling endosome membrane0.0448995149596783
GO:0055037recycling endosome0.0458063293216049
GO:0045296cadherin binding0.0458063293216049
GO:0050839cell adhesion molecule binding0.0458063293216049
GO:0016020membrane0.0458063293216049



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
telencephalon2.78e-10034
cerebral hemisphere1.36e-9732
regional part of cerebral cortex1.93e-9422
regional part of telencephalon1.53e-8832
brain grey matter2.89e-8334
gray matter2.89e-8334
cerebral cortex3.68e-8325
pallium3.68e-8325
regional part of forebrain6.66e-8341
forebrain6.66e-8341
anterior neural tube6.66e-8341
future forebrain6.66e-8341
neocortex7.12e-8220
regional part of nervous system2.55e-6953
regional part of brain2.55e-6953
neural tube1.88e-6556
neural rod1.88e-6556
future spinal cord1.88e-6556
neural keel1.88e-6556
brain2.44e-6268
future brain2.44e-6268
central nervous system2.78e-5681
pre-chordal neural plate7.53e-5561
nervous system2.40e-5089
neural plate1.24e-4382
presumptive neural plate1.24e-4382
gyrus1.66e-416
neurectoderm1.97e-4186
adult organism7.70e-40114
limbic system4.45e-355
ecto-epithelium1.35e-33104
structure with developmental contribution from neural crest4.19e-28132
temporal lobe1.97e-256
ectoderm-derived structure1.70e-24171
ectoderm1.70e-24171
presumptive ectoderm1.70e-24171
parietal lobe2.50e-225
frontal cortex8.23e-223
organ system subdivision2.30e-19223
basal ganglion3.21e-199
nuclear complex of neuraxis3.21e-199
aggregate regional part of brain3.21e-199
collection of basal ganglia3.21e-199
cerebral subcortex3.21e-199
tube2.79e-16192
corpus striatum7.44e-164
striatum7.44e-164
ventral part of telencephalon7.44e-164
future corpus striatum7.44e-164
amygdala1.54e-152
middle temporal gyrus4.80e-152
middle frontal gyrus6.35e-152
Ammon's horn1.04e-142
lobe parts of cerebral cortex1.04e-142
hippocampal formation1.04e-142
limbic lobe1.04e-142
occipital lobe8.48e-135
organ part1.79e-12218
anatomical conduit3.80e-12240
caudate-putamen7.81e-103
dorsal striatum7.81e-103
anatomical cluster9.62e-10373
telencephalic nucleus2.74e-097
insula1.13e-081
paracentral gyrus1.41e-081
epithelium1.46e-08306
cell layer1.96e-08309
olfactory region2.02e-081
primary subdivision of skull2.02e-081
cranium2.02e-081
neurocranium2.02e-081
chondrocranium2.02e-081
cartilaginous neurocranium2.02e-081
head paraxial mesoderm2.02e-081
nucleus accumbens2.17e-081
ventral striatum2.17e-081
postcentral gyrus2.89e-081
occipital pole3.57e-081
pole of cerebral hemisphere3.57e-081
multi-tissue structure4.71e-08342
putamen5.82e-081
corpus callosum7.16e-081
central nervous system cell part cluster7.16e-081
axon tract7.16e-081
intercerebral commissure7.16e-081
dorsal telencephalic commissure7.16e-081
brain white matter7.16e-081
brain commissure7.16e-081
white matter7.16e-081
nervous system commissure7.16e-081
cerebral hemisphere white matter7.16e-081
neural nucleus2.50e-079
nucleus of brain2.50e-079


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

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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