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Coexpression cluster:C648: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!1.39e-91!56;UBERON:0005068!1.39e-91!56;UBERON:0006241!1.39e-91!56;UBERON:0007135!1.39e-91!56;UBERON:0000073!1.76e-84!53;UBERON:0002616!1.76e-84!53;UBERON:0001893!1.67e-82!34;UBERON:0002780!3.74e-81!41;UBERON:0001890!3.74e-81!41;UBERON:0003080!3.74e-81!41;UBERON:0006240!3.74e-81!41;UBERON:0003528!1.25e-74!34;UBERON:0002020!1.25e-74!34;UBERON:0001869!1.04e-72!32;UBERON:0002791!2.26e-72!32;UBERON:0001017!7.92e-70!81;UBERON:0000955!1.12e-68!68;UBERON:0006238!1.12e-68!68;UBERON:0001016!1.96e-62!89;UBERON:0003075!3.94e-61!82;UBERON:0007284!3.94e-61!82;UBERON:0002346!4.65e-58!86;UBERON:0002619!2.10e-53!22;UBERON:0003056!2.43e-53!61;UBERON:0007023!2.42e-49!114;UBERON:0010371!3.98e-47!104;UBERON:0000956!6.98e-47!25;UBERON:0000203!6.98e-47!25;UBERON:0001950!1.45e-43!20;UBERON:0010314!1.05e-38!132;UBERON:0002420!2.53e-30!9;UBERON:0007245!2.53e-30!9;UBERON:0010009!2.53e-30!9;UBERON:0010011!2.53e-30!9;UBERON:0000454!2.53e-30!9;UBERON:0004121!3.01e-30!171;UBERON:0000924!3.01e-30!171;UBERON:0006601!3.01e-30!171;UBERON:0000125!5.87e-30!9;UBERON:0002308!5.87e-30!9;UBERON:0009663!7.92e-29!7;UBERON:0000200!9.24e-24!6;UBERON:0000369!1.36e-23!4;UBERON:0002435!1.36e-23!4;UBERON:0000204!1.36e-23!4;UBERON:0010082!1.36e-23!4;UBERON:0011216!1.72e-23!223;UBERON:0000025!5.55e-23!192;UBERON:0000349!1.51e-19!5;UBERON:0005383!6.35e-18!3;UBERON:0005382!6.35e-18!3;UBERON:0004111!3.20e-17!240;UBERON:0002298!1.89e-15!6;UBERON:0001871!2.37e-13!6;UBERON:0001954!3.28e-13!2;UBERON:0003022!3.28e-13!2;UBERON:0002421!3.28e-13!2;UBERON:0002600!3.28e-13!2;UBERON:0003076!3.84e-13!15;UBERON:0003057!3.84e-13!15;UBERON:0001873!8.00e-13!2;UBERON:0010122!8.00e-13!2;UBERON:0000064!1.90e-12!218;UBERON:0000483!3.17e-12!306;UBERON:0002771!4.30e-12!2;UBERON:0000119!4.76e-12!309;UBERON:0000477!1.10e-11!373;UBERON:0001872!5.18e-11!5;UBERON:0002021!5.55e-11!5;UBERON:0000481!2.43e-09!342;UBERON:0001896!8.74e-09!3;UBERON:0005290!8.74e-09!3;UBERON:0010096!8.74e-09!3;UBERON:0001870!1.29e-08!3;UBERON:0002240!1.75e-08!3;UBERON:0005174!1.75e-08!3;UBERON:0001137!1.75e-08!3;UBERON:0000988!2.36e-08!3;UBERON:0004733!8.68e-08!12;UBERON:0002028!8.68e-08!12;UBERON:0007277!8.68e-08!12;UBERON:0002336!1.46e-07!1;UBERON:0011215!1.46e-07!1;UBERON:0001018!1.46e-07!1;UBERON:0002473!1.46e-07!1;UBERON:0005340!1.46e-07!1;UBERON:0003544!1.46e-07!1;UBERON:0005970!1.46e-07!1;UBERON:0002316!1.46e-07!1;UBERON:0001020!1.46e-07!1;UBERON:0002437!1.46e-07!1;UBERON:0001882!2.10e-07!1;UBERON:0005403!2.10e-07!1;UBERON:0007190!2.52e-07!1;UBERON:0002581!2.67e-07!1;UBERON:0003112!3.01e-07!1;UBERON:0011158!3.01e-07!1;UBERON:0003128!3.01e-07!1;UBERON:0001703!3.01e-07!1;UBERON:0002241!3.01e-07!1;UBERON:0004761!3.01e-07!1;UBERON:0009617!3.01e-07!1;UBERON:0004732!3.40e-07!13;UBERON:0002022!3.82e-07!1;UBERON:0002902!4.06e-07!1;UBERON:0009899!4.06e-07!1;UBERON:0001874!8.18e-07!1;UBERON:0002038!8.67e-07!1;UBERON:0009661!8.67e-07!1;UBERON:0002950!8.67e-07!1;UBERON:0001891!8.67e-07!1;UBERON:0009616!8.67e-07!1;UBERON:0010286!8.67e-07!1
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|tfbs_overrepresentation_for_novel_motifs=0.208137,0.506671,0.202418,0.320418,0.509452,0.854581,0.385011,1.05123,0.621506,0.120648,0.293498,0.423573,0.231404,0.37489,0.977694,0.187326,0.587543,0.131867,0.534957,0.74987,0.202464,0.300734,0.312425,0.167123,0.238419,0.443987,1.17963,0.310589,0.173154,0.399779,0.275306,0.622056,0.355848,0.234859,0.145955,0.473445,0.143715,0.320003,0.799036,0.965212,0.144976,0.724931,1.5935,0.16875,0.111026,0.226447,0.385972,0.284438,0.529264,0.515273,0.456831,0.396393,1.70327,0.694739,0.841347,0.377467,0.522949,0.348876,0.399478,0.348003,0.660716,0.388062,0.62293,0.561703,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.251183,0.312497,0.123677,0.839414,0.224555,0.205774,1.12583,1.34727,0.609242,0.659074,0.548433,0.560705,0.403653,0.307716,0.789807,0.00329133,0.242764,0.170958,0.480498,1.38705,1.01818,0.763867,0.637885,0.368116,0.510793,0.390718,0.53079,0.67819,0.484706,0.622302,0.803034,0.632556,0.672898,0.590971,0.519171,0.289709,0.576179,0.371864,0.238217,0.15924,0.606372,0.670274,0.575539,0.301413,0.971251,0.439271,0.180319,0.274314,0.527634,1.22955,0.831412,0.478284,0.316671,0.413695,1.0796,0.546713,0.988587,0.642598,0.872646,0.392366,0.76453,0.277675,0.886589,1.05706,1.03079,0.659572,0.270369,0.311068,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,0.52079,0.341558,0.505455,1.68078,0.259186,0.112739,0.110712,0.0123511,0.764896,0.286124,0.387634,1.15881,0.465765,0.160686,0.670668,0.21563,0.951654,1.7677,0.608503,0.21815,0.535644,0.402951,2.29884,0.383837,0.0488937
}}
}}

Revision as of 14:22, 26 November 2012


Full id: C648_caudate_corpus_diencephalon_medulla_occipital_nucleus_thalamus



Phase1 CAGE Peaks

Hg19::chr10:1588921..1588932,+p@chr10:1588921..1588932
+
Hg19::chr10:73479518..73479527,-p5@C10orf105
Hg19::chr10:97236225..97236232,-p@chr10:97236225..97236232
-
Hg19::chr14:33926303..33926307,-p@chr14:33926303..33926307
-
Hg19::chr14:36462819..36462832,+p@chr14:36462819..36462832
+
Hg19::chr14:36462843..36462863,+p@chr14:36462843..36462863
+
Hg19::chr17:72823919..72823924,-p@chr17:72823919..72823924
-
Hg19::chr18:24521807..24521809,+p@chr18:24521807..24521809
+
Hg19::chr2:115219219..115219230,+p7@DPP10
Hg19::chr2:232548018..232548022,-p@chr2:232548018..232548022
-
Hg19::chr5:60927228..60927236,-p3@BC032909
p3@BC032910
Hg19::chr9:87605893..87605904,+p@chr9:87605893..87605904
+
Hg19::chr9:87655746..87655753,-p@chr9:87655746..87655753
-


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:0004274dipeptidyl-peptidase IV activity0.0041014168530947
GO:0016806dipeptidyl-peptidase and tripeptidyl-peptidase activity0.0041014168530947
GO:0008239dipeptidyl-peptidase activity0.0041014168530947
GO:0008238exopeptidase activity0.0302749322971859
GO:0008236serine-type peptidase activity0.0406903724635975
GO:0017171serine hydrolase activity0.0406903724635975



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
neural tube1.39e-9156
neural rod1.39e-9156
future spinal cord1.39e-9156
neural keel1.39e-9156
regional part of nervous system1.76e-8453
regional part of brain1.76e-8453
telencephalon1.67e-8234
regional part of forebrain3.74e-8141
forebrain3.74e-8141
anterior neural tube3.74e-8141
future forebrain3.74e-8141
brain grey matter1.25e-7434
gray matter1.25e-7434
cerebral hemisphere1.04e-7232
regional part of telencephalon2.26e-7232
central nervous system7.92e-7081
brain1.12e-6868
future brain1.12e-6868
nervous system1.96e-6289
neural plate3.94e-6182
presumptive neural plate3.94e-6182
neurectoderm4.65e-5886
regional part of cerebral cortex2.10e-5322
pre-chordal neural plate2.43e-5361
adult organism2.42e-49114
ecto-epithelium3.98e-47104
cerebral cortex6.98e-4725
pallium6.98e-4725
neocortex1.45e-4320
structure with developmental contribution from neural crest1.05e-38132
basal ganglion2.53e-309
nuclear complex of neuraxis2.53e-309
aggregate regional part of brain2.53e-309
collection of basal ganglia2.53e-309
cerebral subcortex2.53e-309
ectoderm-derived structure3.01e-30171
ectoderm3.01e-30171
presumptive ectoderm3.01e-30171
neural nucleus5.87e-309
nucleus of brain5.87e-309
telencephalic nucleus7.92e-297
gyrus9.24e-246
corpus striatum1.36e-234
striatum1.36e-234
ventral part of telencephalon1.36e-234
future corpus striatum1.36e-234
organ system subdivision1.72e-23223
tube5.55e-23192
limbic system1.51e-195
caudate-putamen6.35e-183
dorsal striatum6.35e-183
anatomical conduit3.20e-17240
brainstem1.89e-156
temporal lobe2.37e-136
Ammon's horn3.28e-132
lobe parts of cerebral cortex3.28e-132
hippocampal formation3.28e-132
limbic lobe3.28e-132
posterior neural tube3.84e-1315
chordal neural plate3.84e-1315
caudate nucleus8.00e-132
future caudate nucleus8.00e-132
organ part1.90e-12218
epithelium3.17e-12306
middle temporal gyrus4.30e-122
cell layer4.76e-12309
anatomical cluster1.10e-11373
parietal lobe5.18e-115
occipital lobe5.55e-115
multi-tissue structure2.43e-09342
medulla oblongata8.74e-093
myelencephalon8.74e-093
future myelencephalon8.74e-093
frontal cortex1.29e-083
spinal cord1.75e-083
dorsal region element1.75e-083
dorsum1.75e-083
pons2.36e-083
segmental subdivision of hindbrain8.68e-0812
hindbrain8.68e-0812
presumptive hindbrain8.68e-0812
corpus callosum1.46e-071
central nervous system cell part cluster1.46e-071
axon tract1.46e-071
intercerebral commissure1.46e-071
dorsal telencephalic commissure1.46e-071
brain white matter1.46e-071
brain commissure1.46e-071
white matter1.46e-071
nervous system commissure1.46e-071
cerebral hemisphere white matter1.46e-071
nucleus accumbens2.10e-071
ventral striatum2.10e-071
paracentral gyrus2.52e-071
postcentral gyrus2.67e-071
olfactory region3.01e-071
primary subdivision of skull3.01e-071
cranium3.01e-071
neurocranium3.01e-071
chondrocranium3.01e-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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