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Coexpression cluster:C989: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!4.95e-100!56;UBERON:0005068!4.95e-100!56;UBERON:0006241!4.95e-100!56;UBERON:0007135!4.95e-100!56;UBERON:0001016!4.04e-93!89;UBERON:0000073!4.33e-93!53;UBERON:0002616!4.33e-93!53;UBERON:0001017!1.33e-91!81;UBERON:0002780!5.02e-80!41;UBERON:0001890!5.02e-80!41;UBERON:0003080!5.02e-80!41;UBERON:0006240!5.02e-80!41;UBERON:0000955!4.29e-75!68;UBERON:0006238!4.29e-75!68;UBERON:0003075!7.20e-70!82;UBERON:0007284!7.20e-70!82;UBERON:0002346!1.33e-68!86;UBERON:0003528!1.63e-65!34;UBERON:0002020!1.63e-65!34;UBERON:0001893!2.58e-65!34;UBERON:0002791!4.38e-61!32;UBERON:0001869!6.35e-61!32;UBERON:0003056!2.75e-56!61;UBERON:0007023!2.93e-56!114;UBERON:0010371!4.55e-54!104;UBERON:0002619!1.25e-47!22;UBERON:0004121!8.90e-46!171;UBERON:0000924!8.90e-46!171;UBERON:0006601!8.90e-46!171;UBERON:0000956!5.49e-45!25;UBERON:0000203!5.49e-45!25;UBERON:0001950!4.30e-43!20;UBERON:0010314!5.22e-43!132;UBERON:0011216!2.69e-40!223;UBERON:0000025!2.82e-22!192;UBERON:0002420!2.91e-22!9;UBERON:0007245!2.91e-22!9;UBERON:0010009!2.91e-22!9;UBERON:0010011!2.91e-22!9;UBERON:0000454!2.91e-22!9;UBERON:0000125!8.41e-22!9;UBERON:0002308!8.41e-22!9;UBERON:0000477!6.50e-21!373;UBERON:0003076!2.31e-20!15;UBERON:0003057!2.31e-20!15;UBERON:0009663!1.55e-17!7;UBERON:0004732!1.68e-16!13;UBERON:0001894!1.21e-15!7;UBERON:0006222!1.21e-15!7;UBERON:0004111!5.63e-15!240;UBERON:0000200!1.02e-14!6;UBERON:0004733!2.53e-14!12;UBERON:0002028!2.53e-14!12;UBERON:0007277!2.53e-14!12;UBERON:0002298!1.22e-13!6;UBERON:0000349!6.94e-13!5;UBERON:0001871!1.00e-12!6;UBERON:0002021!1.09e-12!5;UBERON:0001872!2.13e-12!5;UBERON:0000064!2.25e-12!218;UBERON:0000481!4.56e-12!342;UBERON:0000483!2.54e-11!306;UBERON:0000119!4.50e-11!309;UBERON:0000369!1.12e-10!4;UBERON:0002435!1.12e-10!4;UBERON:0000204!1.12e-10!4;UBERON:0010082!1.12e-10!4;UBERON:0002784!5.64e-10!4;UBERON:0000922!6.03e-10!592;UBERON:0005423!2.64e-09!581;UBERON:0000923!2.94e-09!560;UBERON:0010316!2.94e-09!560;UBERON:0005291!2.94e-09!560;UBERON:0006598!2.94e-09!560;UBERON:0010317!2.94e-09!560;UBERON:0002532!2.94e-09!560;UBERON:0002050!4.67e-09!564;UBERON:0002680!5.27e-09!9;UBERON:0001895!5.27e-09!9;UBERON:0010092!5.27e-09!9;UBERON:0003296!5.65e-09!4;UBERON:0010133!5.65e-09!4;UBERON:0005383!1.13e-08!3;UBERON:0005382!1.13e-08!3;UBERON:0001870!2.65e-08!3;UBERON:0000062!3.31e-08!503;UBERON:0002240!3.63e-08!3;UBERON:0005174!3.63e-08!3;UBERON:0001137!3.63e-08!3;UBERON:0000988!8.48e-08!3;UBERON:0001896!1.65e-07!3;UBERON:0005290!1.65e-07!3;UBERON:0010096!1.65e-07!3;UBERON:0000467!2.49e-07!624;UBERON:0000480!2.75e-07!625;UBERON:0000468!4.97e-07!656
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.183537,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,0.555925,1.41657,0.450635,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.491486,0.950453,0.341703,0.047825,0.472508,0.29709,0.385586,0.619829,0.135503,0.470396,0.822672,0.388322,1.09762,0.810962,0.628961,0.154814,0.269459,0.570077,0.266487,0.481208,0.685417,0.174436,0.268162,0.413601,1.18362,0.299183,0.386203,0.371118,0.555735,0.440085,0.186577,0.304949,0.63387,0.567337,0.0927889,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,0.304852,1.03748,0.891424,0.429044,0.799673,0.730167,0.797419,0.379656,0.96869,0.745864,0.575394,0.19474,0.986227,0.0958904,0.0757344,0.378318,0.659621,1.59442,1.22073,0.959334,0.827657,0.644398,0.302606,0.239285,1.51085,0.87,0.664183,0.703156,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.732093,0.518187,0.428232,0.710479,1.2139,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,1.08503,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,0.0510299,0.960402,1.03091,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,1.15008,0.553354,0.273194
}}
}}

Revision as of 14:36, 26 November 2012


Full id: C989_optic_globus_medial_thalamus_spinal_occipital_parietal



Phase1 CAGE Peaks

Hg19::chr11:117304153..117304157,-p@chr11:117304153..117304157
-
Hg19::chr11:40315134..40315154,-p10@LRRC4C
Hg19::chr12:123319279..123319305,+p2@HIP1R
Hg19::chr13:78320835..78320853,+p@chr13:78320835..78320853
+
Hg19::chr16:1031491..1031496,-p7@LMF1
Hg19::chr20:58179554..58179578,+p2@PHACTR3
Hg19::chr20:58179582..58179601,+p1@PHACTR3
Hg19::chr8:3014504..3014509,-p@chr8:3014504..3014509
-


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:0003779actin binding0.0326377961348001
GO:0008092cytoskeletal protein binding0.0326377961348001
GO:0050770regulation of axonogenesis0.0362675180022866
GO:0004864protein phosphatase inhibitor activity0.0362675180022866
GO:0019212phosphatase inhibitor activity0.0362675180022866
GO:0050767regulation of neurogenesis0.0362675180022866
GO:0005905coated pit0.0362675180022866
GO:0016363nuclear matrix0.0362675180022866



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
neuronal stem cell3.75e-078
Uber Anatomy
Ontology termp-valuen
neural tube4.95e-10056
neural rod4.95e-10056
future spinal cord4.95e-10056
neural keel4.95e-10056
nervous system4.04e-9389
regional part of nervous system4.33e-9353
regional part of brain4.33e-9353
central nervous system1.33e-9181
regional part of forebrain5.02e-8041
forebrain5.02e-8041
anterior neural tube5.02e-8041
future forebrain5.02e-8041
brain4.29e-7568
future brain4.29e-7568
neural plate7.20e-7082
presumptive neural plate7.20e-7082
neurectoderm1.33e-6886
brain grey matter1.63e-6534
gray matter1.63e-6534
telencephalon2.58e-6534
regional part of telencephalon4.38e-6132
cerebral hemisphere6.35e-6132
pre-chordal neural plate2.75e-5661
adult organism2.93e-56114
ecto-epithelium4.55e-54104
regional part of cerebral cortex1.25e-4722
ectoderm-derived structure8.90e-46171
ectoderm8.90e-46171
presumptive ectoderm8.90e-46171
cerebral cortex5.49e-4525
pallium5.49e-4525
neocortex4.30e-4320
structure with developmental contribution from neural crest5.22e-43132
organ system subdivision2.69e-40223
tube2.82e-22192
basal ganglion2.91e-229
nuclear complex of neuraxis2.91e-229
aggregate regional part of brain2.91e-229
collection of basal ganglia2.91e-229
cerebral subcortex2.91e-229
neural nucleus8.41e-229
nucleus of brain8.41e-229
anatomical cluster6.50e-21373
posterior neural tube2.31e-2015
chordal neural plate2.31e-2015
telencephalic nucleus1.55e-177
segmental subdivision of nervous system1.68e-1613
diencephalon1.21e-157
future diencephalon1.21e-157
anatomical conduit5.63e-15240
gyrus1.02e-146
segmental subdivision of hindbrain2.53e-1412
hindbrain2.53e-1412
presumptive hindbrain2.53e-1412
brainstem1.22e-136
limbic system6.94e-135
temporal lobe1.00e-126
occipital lobe1.09e-125
parietal lobe2.13e-125
organ part2.25e-12218
multi-tissue structure4.56e-12342
epithelium2.54e-11306
cell layer4.50e-11309
corpus striatum1.12e-104
striatum1.12e-104
ventral part of telencephalon1.12e-104
future corpus striatum1.12e-104
regional part of diencephalon5.64e-104
embryo6.03e-10592
developing anatomical structure2.64e-09581
germ layer2.94e-09560
germ layer / neural crest2.94e-09560
embryonic tissue2.94e-09560
presumptive structure2.94e-09560
germ layer / neural crest derived structure2.94e-09560
epiblast (generic)2.94e-09560
embryonic structure4.67e-09564
regional part of metencephalon5.27e-099
metencephalon5.27e-099
future metencephalon5.27e-099
gland of diencephalon5.65e-094
neuroendocrine gland5.65e-094
caudate-putamen1.13e-083
dorsal striatum1.13e-083
frontal cortex2.65e-083
organ3.31e-08503
spinal cord3.63e-083
dorsal region element3.63e-083
dorsum3.63e-083
pons8.48e-083
medulla oblongata1.65e-073
myelencephalon1.65e-073
future myelencephalon1.65e-073
anatomical system2.49e-07624
anatomical group2.75e-07625
multi-cellular organism4.97e-07656


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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