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Coexpression cluster:C1027: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!5.69e-82!56;UBERON:0005068!5.69e-82!56;UBERON:0006241!5.69e-82!56;UBERON:0007135!5.69e-82!56;UBERON:0000073!1.39e-75!53;UBERON:0002616!1.39e-75!53;UBERON:0001017!3.42e-67!81;UBERON:0003075!7.98e-67!82;UBERON:0007284!7.98e-67!82;UBERON:0002780!1.73e-66!41;UBERON:0001890!1.73e-66!41;UBERON:0003080!1.73e-66!41;UBERON:0006240!1.73e-66!41;UBERON:0000955!2.08e-63!68;UBERON:0006238!2.08e-63!68;UBERON:0002346!5.59e-63!86;UBERON:0007023!1.54e-62!114;UBERON:0001016!1.05e-61!89;UBERON:0003528!2.55e-61!34;UBERON:0002020!2.55e-61!34;UBERON:0001893!2.10e-60!34;UBERON:0002791!4.90e-57!32;UBERON:0001869!1.07e-56!32;UBERON:0010371!2.89e-53!104;UBERON:0003056!1.39e-48!61;UBERON:0010314!1.51e-43!132;UBERON:0000956!7.94e-43!25;UBERON:0000203!7.94e-43!25;UBERON:0002619!5.29e-38!22;UBERON:0001950!1.17e-33!20;UBERON:0004121!1.48e-33!171;UBERON:0000924!1.48e-33!171;UBERON:0006601!1.48e-33!171;UBERON:0000025!2.09e-24!192;UBERON:0011216!1.82e-23!223;UBERON:0000125!1.04e-19!9;UBERON:0002308!1.04e-19!9;UBERON:0002420!1.29e-19!9;UBERON:0007245!1.29e-19!9;UBERON:0010009!1.29e-19!9;UBERON:0010011!1.29e-19!9;UBERON:0000454!1.29e-19!9;UBERON:0004111!7.13e-19!240;UBERON:0000483!2.07e-17!306;UBERON:0000119!4.61e-17!309;UBERON:0000477!1.31e-16!373;UBERON:0003076!2.80e-16!15;UBERON:0003057!2.80e-16!15;UBERON:0009663!1.45e-15!7;UBERON:0000481!3.20e-14!342;UBERON:0002298!2.11e-13!6;UBERON:0000200!7.64e-13!6;UBERON:0004732!1.02e-12!13;UBERON:0000349!8.05e-12!5;UBERON:0000064!9.64e-12!218;UBERON:0002021!2.80e-11!5;UBERON:0001871!3.33e-11!6;UBERON:0004733!7.45e-11!12;UBERON:0002028!7.45e-11!12;UBERON:0007277!7.45e-11!12;UBERON:0000369!2.57e-09!4;UBERON:0002435!2.57e-09!4;UBERON:0000204!2.57e-09!4;UBERON:0010082!2.57e-09!4;UBERON:0002784!3.24e-09!4;UBERON:0000062!3.60e-08!503;UBERON:0001894!6.86e-08!7;UBERON:0006222!6.86e-08!7;UBERON:0002240!8.28e-08!3;UBERON:0005174!8.28e-08!3;UBERON:0001137!8.28e-08!3;UBERON:0000988!1.26e-07!3;UBERON:0005383!1.31e-07!3;UBERON:0005382!1.31e-07!3;UBERON:0001896!1.94e-07!3;UBERON:0005290!1.94e-07!3;UBERON:0010096!1.94e-07!3;UBERON:0001870!2.20e-07!3;UBERON:0001872!3.39e-07!5;UBERON:0003978!3.91e-07!3;UBERON:0009751!3.91e-07!3;UBERON:0000946!3.91e-07!3;UBERON:0002523!3.91e-07!3;UBERON:0005983!3.91e-07!3;UBERON:0002165!3.91e-07!3;UBERON:0002062!3.91e-07!3;UBERON:0007280!3.91e-07!3;UBERON:0000922!4.16e-07!592;UBERON:0002050!5.05e-07!564;UBERON:0006947!5.45e-07!3;UBERON:0004054!5.45e-07!3
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,0.481684,1.48054,0.480078,0.554663,0.561282,0.190005,0.0394821,0.450635,0.597407,0.152895,0.543352,0.81316,0.322799,0.774423,0.698835,0.163559,0.0766963,0.341703,0.405031,0.472508,0.805193,0.385586,0.619829,0.135503,0.470396,0.304828,0.388322,0.429397,0.810962,0.220667,0.154814,0.269459,0.0137136,0.266487,0.481208,0.685417,0.174436,0.268162,0.413601,0.0547276,0.299183,0.0169887,0.371118,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,0.85167,0.558065,0.556977,0.746929,0.575742,0.712797,2.54508,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.138565,0.401476,0.730167,0.797419,0.989108,0.96869,0.745864,1.40937,0.19474,0.986227,0.0958904,0.26222,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.644398,0.302606,0.239285,0.488357,0.87,0.664183,0.106284,1.27523,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.116216,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,1.35238,0.83262,1.07171,0.674618,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,1.05631,0.224241,0.283443,0.0510299,0.960402,0.183004,1.37178,1.36372,0.643609,0.288769,1.00225,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,0.553354,0.146591
}}
}}

Revision as of 14:38, 26 November 2012


Full id: C1027_hippocampus_occipital_optic_globus_thalamus_cerebral_locus



Phase1 CAGE Peaks

Hg19::chr13:66878571..66878580,-p@chr13:66878571..66878580
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Hg19::chr13:98045526..98045628,+p@chr13:98045526..98045628
+
Hg19::chr1:109856117..109856176,-p@chr1:109856117..109856176
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Hg19::chr1:109856200..109856211,-p@chr1:109856200..109856211
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Hg19::chr1:155851487..155851498,+p@chr1:155851487..155851498
+
Hg19::chr3:58551136..58551152,-p@chr3:58551136..58551152
-
Hg19::chrX:13789494..13789511,-p@chrX:13789494..13789511
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Hg19::chrX:13789649..13789660,-p@chrX:13789649..13789660
-


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 tube5.69e-8256
neural rod5.69e-8256
future spinal cord5.69e-8256
neural keel5.69e-8256
regional part of nervous system1.39e-7553
regional part of brain1.39e-7553
central nervous system3.42e-6781
neural plate7.98e-6782
presumptive neural plate7.98e-6782
regional part of forebrain1.73e-6641
forebrain1.73e-6641
anterior neural tube1.73e-6641
future forebrain1.73e-6641
brain2.08e-6368
future brain2.08e-6368
neurectoderm5.59e-6386
adult organism1.54e-62114
nervous system1.05e-6189
brain grey matter2.55e-6134
gray matter2.55e-6134
telencephalon2.10e-6034
regional part of telencephalon4.90e-5732
cerebral hemisphere1.07e-5632
ecto-epithelium2.89e-53104
pre-chordal neural plate1.39e-4861
structure with developmental contribution from neural crest1.51e-43132
cerebral cortex7.94e-4325
pallium7.94e-4325
regional part of cerebral cortex5.29e-3822
neocortex1.17e-3320
ectoderm-derived structure1.48e-33171
ectoderm1.48e-33171
presumptive ectoderm1.48e-33171
tube2.09e-24192
organ system subdivision1.82e-23223
neural nucleus1.04e-199
nucleus of brain1.04e-199
basal ganglion1.29e-199
nuclear complex of neuraxis1.29e-199
aggregate regional part of brain1.29e-199
collection of basal ganglia1.29e-199
cerebral subcortex1.29e-199
anatomical conduit7.13e-19240
epithelium2.07e-17306
cell layer4.61e-17309
anatomical cluster1.31e-16373
posterior neural tube2.80e-1615
chordal neural plate2.80e-1615
telencephalic nucleus1.45e-157
multi-tissue structure3.20e-14342
brainstem2.11e-136
gyrus7.64e-136
segmental subdivision of nervous system1.02e-1213
limbic system8.05e-125
organ part9.64e-12218
occipital lobe2.80e-115
temporal lobe3.33e-116
segmental subdivision of hindbrain7.45e-1112
hindbrain7.45e-1112
presumptive hindbrain7.45e-1112
corpus striatum2.57e-094
striatum2.57e-094
ventral part of telencephalon2.57e-094
future corpus striatum2.57e-094
regional part of diencephalon3.24e-094
organ3.60e-08503
diencephalon6.86e-087
future diencephalon6.86e-087
spinal cord8.28e-083
dorsal region element8.28e-083
dorsum8.28e-083
pons1.26e-073
caudate-putamen1.31e-073
dorsal striatum1.31e-073
medulla oblongata1.94e-073
myelencephalon1.94e-073
future myelencephalon1.94e-073
frontal cortex2.20e-073
parietal lobe3.39e-075
valve3.91e-073
cardiac mesenchyme3.91e-073
cardial valve3.91e-073
tunica intima3.91e-073
heart layer3.91e-073
endocardium3.91e-073
endocardial cushion3.91e-073
presumptive endocardium3.91e-073
embryo4.16e-07592
embryonic structure5.05e-07564
male genital duct5.45e-073
internal male genitalia5.45e-073


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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