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Coexpression cluster:C1123: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.0232809,0.384703,0.529489,0.343148,0.52784,0.604235,0.643217,0.637583,0.0544999,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.28906,0.19568,0.66776,0.384762,0.23059,0.520063,0.897212,0.430372,0.670692,0.49486,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.021349,0.305874,0.529001,0.282922,0.207499,0.829015,0.459366,0.0729319,0.902101,0.0257952,0.415364,0.60533,0.486696,0.511111,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.656075,0.115253,1.0929,0.179863,0.168304,0.156354,0.782748,0.850825,0.424224,0.580264,0.798651,0.625403,0.649554,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.566252,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.821533,0.039977,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,2.78754,2.10682,1.70417,1.21002,1.4603,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.695791,0.602897,0.00626991
}}
}}

Revision as of 14:42, 26 November 2012


Full id: C1123_medial_middle_parietal_occipital_paracentral_frontal_cerebral



Phase1 CAGE Peaks

Hg19::chr10:79383809..79383833,+p@chr10:79383809..79383833
+
Hg19::chr12:90987338..90987355,+p@chr12:90987338..90987355
+
Hg19::chr2:175757825..175757858,-p@chr2:175757825..175757858
-
Hg19::chr2:86707317..86707337,+p@chr2:86707317..86707337
+
Hg19::chr4:146071958..146071961,-p15@OTUD4
Hg19::chr8:27606125..27606134,-p6@CCDC25
Hg19::chr8:27606152..27606165,-p3@CCDC25


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

No GOStat results

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
telencephalon2.36e-7834
brain grey matter5.23e-7834
gray matter5.23e-7834
regional part of forebrain5.22e-7741
forebrain5.22e-7741
anterior neural tube5.22e-7741
future forebrain5.22e-7741
neural tube3.80e-7656
neural rod3.80e-7656
future spinal cord3.80e-7656
neural keel3.80e-7656
cerebral hemisphere6.03e-7632
regional part of telencephalon1.30e-7532
regional part of nervous system9.08e-7553
regional part of brain9.08e-7553
central nervous system1.60e-6781
brain6.16e-6668
future brain6.16e-6668
nervous system2.24e-6089
regional part of cerebral cortex7.25e-5622
neocortex1.38e-5320
neural plate1.22e-5082
presumptive neural plate1.22e-5082
pre-chordal neural plate1.31e-5061
cerebral cortex4.62e-4925
pallium4.62e-4925
neurectoderm4.58e-4886
adult organism1.41e-47114
ecto-epithelium6.59e-39104
gyrus4.73e-376
structure with developmental contribution from neural crest1.50e-34132
basal ganglion2.78e-319
nuclear complex of neuraxis2.78e-319
aggregate regional part of brain2.78e-319
collection of basal ganglia2.78e-319
cerebral subcortex2.78e-319
neural nucleus3.83e-319
nucleus of brain3.83e-319
telencephalic nucleus6.64e-307
ectoderm-derived structure2.87e-29171
ectoderm2.87e-29171
presumptive ectoderm2.87e-29171
organ system subdivision8.58e-23223
frontal cortex1.88e-193
tube1.11e-18192
temporal lobe4.76e-146
corpus striatum5.08e-144
striatum5.08e-144
ventral part of telencephalon5.08e-144
future corpus striatum5.08e-144
anatomical conduit7.35e-14240
middle frontal gyrus1.08e-132
middle temporal gyrus1.22e-132
globus pallidus6.32e-132
pallidum6.32e-132
meninx1.45e-122
membrane organ1.45e-122
meningeal cluster1.45e-122
organ part6.57e-12218
parietal lobe9.06e-125
anatomical cluster2.34e-11373
limbic system3.63e-115
occipital lobe4.03e-115
epithelium1.11e-09306
cell layer1.56e-09309
brainstem5.46e-096
caudate-putamen6.59e-093
dorsal striatum6.59e-093
pons1.75e-083
multi-tissue structure4.68e-08342
paracentral gyrus1.44e-071
olfactory region1.85e-071
primary subdivision of skull1.85e-071
cranium1.85e-071
neurocranium1.85e-071
chondrocranium1.85e-071
cartilaginous neurocranium1.85e-071
head paraxial mesoderm1.85e-071
postcentral gyrus2.09e-071
nucleus accumbens2.67e-071
ventral striatum2.67e-071
putamen2.84e-071
insula3.02e-071
substantia nigra4.89e-071
midbrain nucleus4.89e-071
regional part of midbrain4.89e-071
midbrain4.89e-071
presumptive midbrain4.89e-071
midbrain neural tube4.89e-071
occipital pole5.84e-071
pole of cerebral hemisphere5.84e-071
dura mater6.97e-071
future meninx6.97e-071
ectomeninx6.97e-071
future dura mater6.97e-071


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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