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Coexpression cluster:C4632: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001869!1.56e-65!32;UBERON:0001893!3.01e-65!34;UBERON:0003056!2.98e-62!61;UBERON:0002791!2.27e-61!32;UBERON:0003528!2.54e-57!34;UBERON:0002020!2.54e-57!34;UBERON:0002780!3.23e-56!41;UBERON:0001890!3.23e-56!41;UBERON:0003080!3.23e-56!41;UBERON:0006240!3.23e-56!41;UBERON:0000956!2.33e-55!25;UBERON:0000203!2.33e-55!25;UBERON:0002619!3.57e-48!22;UBERON:0001950!1.09e-43!20;UBERON:0003075!2.90e-43!82;UBERON:0007284!2.90e-43!82;UBERON:0001017!2.25e-42!81;UBERON:0000073!1.86e-41!53;UBERON:0002616!1.86e-41!53;UBERON:0002346!1.08e-40!86;UBERON:0001016!7.15e-39!89;UBERON:0010371!8.94e-39!104;UBERON:0001049!9.63e-39!56;UBERON:0005068!9.63e-39!56;UBERON:0006241!9.63e-39!56;UBERON:0007135!9.63e-39!56;UBERON:0000955!2.73e-36!68;UBERON:0006238!2.73e-36!68;UBERON:0004121!6.23e-30!171;UBERON:0000924!6.23e-30!171;UBERON:0006601!6.23e-30!171;UBERON:0010314!4.40e-25!132;UBERON:0000200!1.53e-14!6;UBERON:0011216!6.23e-14!223;UBERON:0002021!3.92e-13!5;UBERON:0001871!4.50e-13!6;UBERON:0000064!1.07e-12!218;UBERON:0007625!1.12e-12!11;UBERON:0000349!1.26e-12!5;UBERON:0002420!1.37e-12!9;UBERON:0007245!1.37e-12!9;UBERON:0010009!1.37e-12!9;UBERON:0010011!1.37e-12!9;UBERON:0000454!1.37e-12!9;UBERON:0001872!1.72e-12!5;UBERON:0007023!4.42e-12!114;UBERON:0000970!4.84e-11!21;UBERON:0002104!4.84e-11!21;UBERON:0000369!7.94e-10!4;UBERON:0002435!7.94e-10!4;UBERON:0000204!7.94e-10!4;UBERON:0010082!7.94e-10!4;UBERON:0000966!8.24e-10!6;UBERON:0005388!8.24e-10!6;UBERON:0001802!8.24e-10!6;UBERON:0000019!1.06e-09!20;UBERON:0000047!1.06e-09!20;UBERON:0010312!1.06e-09!20;UBERON:0004088!1.06e-09!20;UBERON:0010230!1.06e-09!20;UBERON:0003072!1.06e-09!20;UBERON:0004128!1.06e-09!20;UBERON:0003071!1.06e-09!20;UBERON:0000020!2.33e-09!24;UBERON:0001032!2.33e-09!24;UBERON:0004456!2.33e-09!24;UBERON:0000477!2.36e-09!373;UBERON:0000488!2.50e-09!4;UBERON:0001456!1.25e-08!22;UBERON:0009663!2.24e-08!7;UBERON:0001782!2.81e-08!3;UBERON:0005424!2.81e-08!3;UBERON:0001870!3.58e-08!3;UBERON:0005383!6.21e-08!3;UBERON:0005382!6.21e-08!3;UBERON:0000483!9.35e-08!306;UBERON:0001778!1.41e-07!3;UBERON:0001775!1.41e-07!3;UBERON:0000119!1.45e-07!309;UBERON:0000025!7.66e-07!192
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.11328,0.925331,1.54465,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,2.36218,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135
}}
}}

Revision as of 16:51, 26 November 2012


Full id: C4632_Neurons_parietal_medial_Neural_occipital_Astrocyte_duodenum



Phase1 CAGE Peaks

Hg19::chr6:98264571..98264591,+p@chr6:98264571..98264591
+
Hg19::chr9:126777702..126777716,+p5@LHX2
Hg19::chr9:126794936..126794940,+p@chr9:126794936..126794940
+


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

Uber Anatomy
Ontology termp-valuen
cerebral hemisphere1.56e-6532
telencephalon3.01e-6534
pre-chordal neural plate2.98e-6261
regional part of telencephalon2.27e-6132
brain grey matter2.54e-5734
gray matter2.54e-5734
regional part of forebrain3.23e-5641
forebrain3.23e-5641
anterior neural tube3.23e-5641
future forebrain3.23e-5641
cerebral cortex2.33e-5525
pallium2.33e-5525
regional part of cerebral cortex3.57e-4822
neocortex1.09e-4320
neural plate2.90e-4382
presumptive neural plate2.90e-4382
central nervous system2.25e-4281
regional part of nervous system1.86e-4153
regional part of brain1.86e-4153
neurectoderm1.08e-4086
nervous system7.15e-3989
ecto-epithelium8.94e-39104
neural tube9.63e-3956
neural rod9.63e-3956
future spinal cord9.63e-3956
neural keel9.63e-3956
brain2.73e-3668
future brain2.73e-3668
ectoderm-derived structure6.23e-30171
ectoderm6.23e-30171
presumptive ectoderm6.23e-30171
structure with developmental contribution from neural crest4.40e-25132
gyrus1.53e-146
organ system subdivision6.23e-14223
occipital lobe3.92e-135
temporal lobe4.50e-136
organ part1.07e-12218
pigment epithelium of eye1.12e-1211
limbic system1.26e-125
basal ganglion1.37e-129
nuclear complex of neuraxis1.37e-129
aggregate regional part of brain1.37e-129
collection of basal ganglia1.37e-129
cerebral subcortex1.37e-129
parietal lobe1.72e-125
adult organism4.42e-12114
eye4.84e-1121
visual system4.84e-1121
corpus striatum7.94e-104
striatum7.94e-104
ventral part of telencephalon7.94e-104
future corpus striatum7.94e-104
retina8.24e-106
photoreceptor array8.24e-106
posterior segment of eyeball8.24e-106
camera-type eye1.06e-0920
simple eye1.06e-0920
immature eye1.06e-0920
ocular region1.06e-0920
eyeball of camera-type eye1.06e-0920
optic cup1.06e-0920
optic vesicle1.06e-0920
eye primordium1.06e-0920
sense organ2.33e-0924
sensory system2.33e-0924
entire sense organ system2.33e-0924
anatomical cluster2.36e-09373
atypical epithelium2.50e-094
face1.25e-0822
telencephalic nucleus2.24e-087
pigmented layer of retina2.81e-083
presumptive retinal pigmented epithelium2.81e-083
frontal cortex3.58e-083
caudate-putamen6.21e-083
dorsal striatum6.21e-083
epithelium9.35e-08306
ciliary epithelium1.41e-073
ciliary body1.41e-073
cell layer1.45e-07309
tube7.66e-07192


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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