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Coexpression cluster:C1008: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!4.31e-77!56;UBERON:0005068!4.31e-77!56;UBERON:0006241!4.31e-77!56;UBERON:0007135!4.31e-77!56;UBERON:0000073!7.86e-75!53;UBERON:0002616!7.86e-75!53;UBERON:0002780!6.22e-60!41;UBERON:0001890!6.22e-60!41;UBERON:0003080!6.22e-60!41;UBERON:0006240!6.22e-60!41;UBERON:0003528!7.78e-58!34;UBERON:0002020!7.78e-58!34;UBERON:0000955!7.50e-57!68;UBERON:0006238!7.50e-57!68;UBERON:0003075!2.36e-56!82;UBERON:0007284!2.36e-56!82;UBERON:0002791!3.38e-54!32;UBERON:0002346!1.40e-53!86;UBERON:0001017!1.00e-51!81;UBERON:0001893!6.17e-51!34;UBERON:0001016!1.87e-50!89;UBERON:0001869!1.77e-47!32;UBERON:0003056!3.89e-44!61;UBERON:0010371!1.03e-43!104;UBERON:0007023!5.74e-40!114;UBERON:0000125!1.40e-39!9;UBERON:0002308!1.40e-39!9;UBERON:0002420!2.10e-39!9;UBERON:0007245!2.10e-39!9;UBERON:0010009!2.10e-39!9;UBERON:0010011!2.10e-39!9;UBERON:0000454!2.10e-39!9;UBERON:0009663!1.87e-37!7;UBERON:0010314!1.52e-36!132;UBERON:0002619!1.52e-30!22;UBERON:0001950!4.08e-27!20;UBERON:0000956!7.73e-27!25;UBERON:0000203!7.73e-27!25;UBERON:0004121!9.29e-25!171;UBERON:0000924!9.29e-25!171;UBERON:0006601!9.29e-25!171;UBERON:0005383!1.38e-22!3;UBERON:0005382!1.38e-22!3;UBERON:0004732!2.23e-20!13;UBERON:0000025!6.31e-20!192;UBERON:0000200!7.49e-20!6;UBERON:0011216!1.08e-19!223;UBERON:0003076!1.50e-17!15;UBERON:0003057!1.50e-17!15;UBERON:0000369!4.24e-17!4;UBERON:0002435!4.24e-17!4;UBERON:0000204!4.24e-17!4;UBERON:0010082!4.24e-17!4;UBERON:0001897!4.31e-16!2;UBERON:0010225!4.31e-16!2;UBERON:0001875!5.83e-16!2;UBERON:0006514!5.83e-16!2;UBERON:0001873!7.31e-16!2;UBERON:0010122!7.31e-16!2;UBERON:0002771!8.50e-16!2;UBERON:0002702!1.23e-15!2;UBERON:0004733!1.88e-15!12;UBERON:0002028!1.88e-15!12;UBERON:0007277!1.88e-15!12;UBERON:0004111!4.07e-15!240;UBERON:0002680!2.14e-13!9;UBERON:0001895!2.14e-13!9;UBERON:0010092!2.14e-13!9;UBERON:0000064!1.73e-12!218;UBERON:0000483!3.50e-12!306;UBERON:0000119!5.07e-12!309;UBERON:0002298!7.63e-12!6;UBERON:0000988!8.47e-11!3;UBERON:0001870!9.82e-11!3;UBERON:0000481!2.34e-10!342;UBERON:0001894!3.60e-10!7;UBERON:0006222!3.60e-10!7;UBERON:0001871!3.96e-10!6;UBERON:0000477!4.01e-10!373;UBERON:0000941!3.58e-09!1;UBERON:0001785!3.58e-09!1;UBERON:0002464!3.58e-09!1;UBERON:0004904!3.58e-09!1;UBERON:0001021!3.58e-09!1;UBERON:0003902!3.58e-09!1;UBERON:0005425!3.58e-09!1;UBERON:0002038!9.02e-09!1;UBERON:0009661!9.02e-09!1;UBERON:0002950!9.02e-09!1;UBERON:0001891!9.02e-09!1;UBERON:0009616!9.02e-09!1;UBERON:0010286!9.02e-09!1;UBERON:0003112!1.65e-08!1;UBERON:0011158!1.65e-08!1;UBERON:0003128!1.65e-08!1;UBERON:0001703!1.65e-08!1;UBERON:0002241!1.65e-08!1;UBERON:0004761!1.65e-08!1;UBERON:0009617!1.65e-08!1;UBERON:0002784!1.72e-08!4;UBERON:0001874!1.78e-08!1;UBERON:0000349!5.73e-07!5;UBERON:0001872!6.65e-07!5;UBERON:0002021!7.70e-07!5
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0704539,0.341646,0.481684,0.816074,0.480078,0.554663,0.561282,0.555925,0.154405,0.450635,0.597407,0.152895,0.543352,0.81316,0.322799,0.774423,0.250594,0.491486,0.264925,0.905237,0.405031,0.472508,0.29709,1.00212,0.619829,0.421276,0.470396,0.304828,0.122648,0.429397,0.810962,0.220667,0.154814,0.742281,0.0649851,0.266487,0.481208,0.244807,0.174436,0.268162,0.413601,0.775279,0.299183,0.0775086,0.371118,0.555735,0.440085,0.416595,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.556977,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.138565,0.799673,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,0.19474,0.986227,0.0220225,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.672575,0.162291,0.87,0.664183,0.106284,0.688301,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.116216,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.364369,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,1.35598,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.283443,0.0510299,0.960402,1.03091,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.0643507
}}
}}

Revision as of 14:37, 26 November 2012


Full id: C1008_globus_thalamus_optic_medulla_parietal_caudate_hippocampus



Phase1 CAGE Peaks

Hg19::chr11:98185887..98185890,+p@chr11:98185887..98185890
+
Hg19::chr13:78281161..78281170,+p@chr13:78281161..78281170
+
Hg19::chr1:231945981..231945983,+p@chr1:231945981..231945983
+
Hg19::chr20:40282556..40282558,+p@chr20:40282556..40282558
+
Hg19::chr2:86150436..86150440,+p@chr2:86150436..86150440
+
Hg19::chr3:181459063..181459078,+p@chr3:181459063..181459078
+
Hg19::chr3:47054521..47054522,+p@chr3:47054521..47054522
+
Hg19::chr7:91092835..91092842,+p@chr7:91092835..91092842
+


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
neural tube4.31e-7756
neural rod4.31e-7756
future spinal cord4.31e-7756
neural keel4.31e-7756
regional part of nervous system7.86e-7553
regional part of brain7.86e-7553
regional part of forebrain6.22e-6041
forebrain6.22e-6041
anterior neural tube6.22e-6041
future forebrain6.22e-6041
brain grey matter7.78e-5834
gray matter7.78e-5834
brain7.50e-5768
future brain7.50e-5768
neural plate2.36e-5682
presumptive neural plate2.36e-5682
regional part of telencephalon3.38e-5432
neurectoderm1.40e-5386
central nervous system1.00e-5181
telencephalon6.17e-5134
nervous system1.87e-5089
cerebral hemisphere1.77e-4732
pre-chordal neural plate3.89e-4461
ecto-epithelium1.03e-43104
adult organism5.74e-40114
neural nucleus1.40e-399
nucleus of brain1.40e-399
basal ganglion2.10e-399
nuclear complex of neuraxis2.10e-399
aggregate regional part of brain2.10e-399
collection of basal ganglia2.10e-399
cerebral subcortex2.10e-399
telencephalic nucleus1.87e-377
structure with developmental contribution from neural crest1.52e-36132
regional part of cerebral cortex1.52e-3022
neocortex4.08e-2720
cerebral cortex7.73e-2725
pallium7.73e-2725
ectoderm-derived structure9.29e-25171
ectoderm9.29e-25171
presumptive ectoderm9.29e-25171
caudate-putamen1.38e-223
dorsal striatum1.38e-223
segmental subdivision of nervous system2.23e-2013
tube6.31e-20192
gyrus7.49e-206
organ system subdivision1.08e-19223
posterior neural tube1.50e-1715
chordal neural plate1.50e-1715
corpus striatum4.24e-174
striatum4.24e-174
ventral part of telencephalon4.24e-174
future corpus striatum4.24e-174
dorsal plus ventral thalamus4.31e-162
thalamic complex4.31e-162
globus pallidus5.83e-162
pallidum5.83e-162
caudate nucleus7.31e-162
future caudate nucleus7.31e-162
middle temporal gyrus8.50e-162
middle frontal gyrus1.23e-152
segmental subdivision of hindbrain1.88e-1512
hindbrain1.88e-1512
presumptive hindbrain1.88e-1512
anatomical conduit4.07e-15240
regional part of metencephalon2.14e-139
metencephalon2.14e-139
future metencephalon2.14e-139
organ part1.73e-12218
epithelium3.50e-12306
cell layer5.07e-12309
brainstem7.63e-126
pons8.47e-113
frontal cortex9.82e-113
multi-tissue structure2.34e-10342
diencephalon3.60e-107
future diencephalon3.60e-107
temporal lobe3.96e-106
anatomical cluster4.01e-10373
cranial nerve II3.58e-091
cranial nerve3.58e-091
nerve trunk3.58e-091
nerve connecting eye with brain3.58e-091
nerve3.58e-091
retinal neural layer3.58e-091
presumptive neural retina3.58e-091
substantia nigra9.02e-091
midbrain nucleus9.02e-091
regional part of midbrain9.02e-091
midbrain9.02e-091
presumptive midbrain9.02e-091
midbrain neural tube9.02e-091
olfactory region1.65e-081
primary subdivision of skull1.65e-081
cranium1.65e-081
neurocranium1.65e-081
chondrocranium1.65e-081
cartilaginous neurocranium1.65e-081
head paraxial mesoderm1.65e-081
regional part of diencephalon1.72e-084


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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