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Coexpression cluster:C358: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!7.34e-94!53;UBERON:0002616!7.34e-94!53;UBERON:0001049!1.28e-88!56;UBERON:0005068!1.28e-88!56;UBERON:0006241!1.28e-88!56;UBERON:0007135!1.28e-88!56;UBERON:0000955!4.77e-81!68;UBERON:0006238!4.77e-81!68;UBERON:0003528!1.02e-72!34;UBERON:0002020!1.02e-72!34;UBERON:0002780!1.09e-71!41;UBERON:0001890!1.09e-71!41;UBERON:0003080!1.09e-71!41;UBERON:0006240!1.09e-71!41;UBERON:0001869!3.71e-70!32;UBERON:0001017!2.00e-67!81;UBERON:0001893!6.83e-66!34;UBERON:0002791!1.50e-63!32;UBERON:0003075!3.12e-63!82;UBERON:0007284!3.12e-63!82;UBERON:0001016!3.01e-60!89;UBERON:0002346!4.71e-60!86;UBERON:0002619!6.93e-59!22;UBERON:0001950!1.35e-56!20;UBERON:0000956!1.06e-51!25;UBERON:0000203!1.06e-51!25;UBERON:0003056!3.22e-51!61;UBERON:0010371!9.70e-49!104;UBERON:0010314!5.74e-40!132;UBERON:0007023!2.31e-38!114;UBERON:0004121!5.36e-29!171;UBERON:0000924!5.36e-29!171;UBERON:0006601!5.36e-29!171;UBERON:0011216!3.84e-24!223;UBERON:0000200!2.07e-23!6;UBERON:0002298!6.91e-23!6;UBERON:0004733!3.19e-22!12;UBERON:0002028!3.19e-22!12;UBERON:0007277!3.19e-22!12;UBERON:0000125!5.04e-22!9;UBERON:0002308!5.04e-22!9;UBERON:0000025!5.51e-22!192;UBERON:0004732!1.90e-20!13;UBERON:0001871!4.79e-20!6;UBERON:0002021!4.78e-18!5;UBERON:0003076!1.32e-17!15;UBERON:0003057!1.32e-17!15;UBERON:0000988!2.67e-17!3;UBERON:0004111!2.16e-16!240;UBERON:0002680!9.43e-16!9;UBERON:0001895!9.43e-16!9;UBERON:0010092!9.43e-16!9;UBERON:0000064!9.74e-16!218;UBERON:0002420!1.21e-15!9;UBERON:0007245!1.21e-15!9;UBERON:0010009!1.21e-15!9;UBERON:0010011!1.21e-15!9;UBERON:0000454!1.21e-15!9;UBERON:0000369!2.49e-13!4;UBERON:0002435!2.49e-13!4;UBERON:0000204!2.49e-13!4;UBERON:0010082!2.49e-13!4;UBERON:0009663!4.18e-13!7;UBERON:0000481!1.09e-12!342;UBERON:0000483!1.26e-12!306;UBERON:0002771!1.49e-12!2;UBERON:0000119!1.92e-12!309;UBERON:0002148!2.95e-12!2;UBERON:0006331!2.95e-12!2;UBERON:0009662!2.95e-12!2;UBERON:0000477!5.47e-12!373;UBERON:0000349!7.01e-11!5;UBERON:0001872!1.36e-10!5;UBERON:0001870!1.06e-08!3;UBERON:0005383!1.06e-08!3;UBERON:0005382!1.06e-08!3;UBERON:0001896!2.91e-08!3;UBERON:0005290!2.91e-08!3;UBERON:0010096!2.91e-08!3;UBERON:0001894!7.74e-08!7;UBERON:0006222!7.74e-08!7;UBERON:0003112!3.36e-07!1;UBERON:0011158!3.36e-07!1;UBERON:0003128!3.36e-07!1;UBERON:0001703!3.36e-07!1;UBERON:0002241!3.36e-07!1;UBERON:0004761!3.36e-07!1;UBERON:0009617!3.36e-07!1;UBERON:0001874!4.01e-07!1
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|tfbs_overrepresentation_for_novel_motifs=0.0457572,0.0231511,0.166513,0.690252,0.300153,0.686427,0.143738,0.67282,0.243775,0.218928,0.296543,0.506588,0.0229732,0.137151,0.547249,0.340618,0.292499,0.208248,0.00489602,0.387629,0.674182,0.0110496,0.0988328,0.0295515,0.0595477,0.183961,0.395825,0.322791,0.0317437,0.0421779,0.0782091,0.320373,0.0599945,0.0734639,0.0224141,0.0645311,0.0217109,0.103252,0.198628,0.0327729,0.238421,0.0712053,0.143717,0.861813,0.00211418,0.0539221,0.144369,0.0831196,3.60358,0.129383,0.193102,0.151263,0.117222,0.380845,0.508661,0.138819,0.313641,0.120685,0.0421017,0.120144,0.352258,0.145744,0.244827,0.272031,0.156335,0.247273,0.586135,0.926911,0.839788,0.773993,0.0657842,0.996109,0.0532374,1.26425,0.067299,0.0566402,0.111101,0.259779,0.309955,0.458109,0.192029,0.271247,0.473085,0.685639,0.462965,4.78264e-05,1.84462,0.494212,0.210271,1.02207,0.670213,0.44026,0.886629,1.19564,0.127143,3.73391,0.180218,0.366883,0.213366,0.0295059,1.32255,0.87685,0.362441,0.295241,0.239166,0.0860038,0.283454,0.135201,0.0594507,0.0267912,0.0470467,0.360242,1.02154,0.308638,0.626724,0.442606,0.0751716,0.0776823,0.245619,1.60703,1.24902,1.13226,0.332247,0.489924,0.727676,0.260327,0.432896,0.337232,0.536756,0.191028,0.440837,0.0794722,0.549348,0.484932,0.681963,12.141,1.40984,0.0980487,0.643378,1.46638,1.07263,0.609773,0.435398,0.364073,0.675164,0.371522,0.228804,1.30966,0.0698156,0.0130645,0.0156579,0.00397701,0.441156,0.107215,0.145462,1.88206,0.199535,4.42946,1.73033,0.049033,0.608684,0.425737,0.309357,0.418485,0.251767,0.155652,0.0550646,0.440174,3.87526e-06
}}
}}

Revision as of 14:09, 26 November 2012


Full id: C358_cerebellum_middle_occipital_parietal_pineal_medial_amygdala



Phase1 CAGE Peaks

Hg19::chr11:12189656..12189676,+p@chr11:12189656..12189676
+
Hg19::chr11:132711753..132711754,-p@chr11:132711753..132711754
-
Hg19::chr11:132795109..132795151,-p@chr11:132795109..132795151
-
Hg19::chr11:133818054..133818066,-p@chr11:133818054..133818066
-
Hg19::chr11:133818091..133818133,-p@chr11:133818091..133818133
-
Hg19::chr11:64411144..64411154,-p14@NRXN2
Hg19::chr12:121676126..121676137,-p@chr12:121676126..121676137
-
Hg19::chr12:41233225..41233247,+p@chr12:41233225..41233247
+
Hg19::chr12:41233525..41233536,+p@chr12:41233525..41233536
+
Hg19::chr12:41234328..41234338,+p@chr12:41234328..41234338
+
Hg19::chr13:102919100..102919109,-p@chr13:102919100..102919109
-
Hg19::chr15:91806292..91806298,+p@chr15:91806292..91806298
+
Hg19::chr16:335698..335702,+p@chr16:335698..335702
+
Hg19::chr17:77408529..77408544,-p@chr17:77408529..77408544
-
Hg19::chr19:23507286..23507309,-p@chr19:23507286..23507309
-
Hg19::chr19:36443560..36443561,+p@chr19:36443560..36443561
+
Hg19::chr1:102433144..102433146,-p@chr1:102433144..102433146
-
Hg19::chr1:203015803..203015809,+p@chr1:203015803..203015809
+
Hg19::chr2:180503950..180503954,-p@chr2:180503950..180503954
-
Hg19::chr3:121013244..121013255,+p@chr3:121013244..121013255
+
Hg19::chr4:21558541..21558544,-p@chr4:21558541..21558544
-
Hg19::chr5:136319305..136319309,-p@chr5:136319305..136319309
-
Hg19::chr5:19774915..19774916,-p@chr5:19774915..19774916
-
Hg19::chr8:85139312..85139316,+p@chr8:85139312..85139316
+
Hg19::chr8:85348805..85348809,+p@chr8:85348805..85348809
+
Hg19::chrX:49054728..49054739,-p@chrX:49054728..49054739
-
Hg19::chrX:49054890..49054899,-p@chrX:49054890..49054899
-
Hg19::chrX:49055058..49055077,-p@chrX:49055058..49055077
-
Hg19::chrX:49055109..49055167,-p@chrX:49055109..49055167
-
Hg19::chrX:49055219..49055236,-p@chrX:49055219..49055236
-
Hg19::chrX:49055296..49055306,-p@chrX:49055296..49055306
-


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
regional part of nervous system7.34e-9453
regional part of brain7.34e-9453
neural tube1.28e-8856
neural rod1.28e-8856
future spinal cord1.28e-8856
neural keel1.28e-8856
brain4.77e-8168
future brain4.77e-8168
brain grey matter1.02e-7234
gray matter1.02e-7234
regional part of forebrain1.09e-7141
forebrain1.09e-7141
anterior neural tube1.09e-7141
future forebrain1.09e-7141
cerebral hemisphere3.71e-7032
central nervous system2.00e-6781
telencephalon6.83e-6634
regional part of telencephalon1.50e-6332
neural plate3.12e-6382
presumptive neural plate3.12e-6382
nervous system3.01e-6089
neurectoderm4.71e-6086
regional part of cerebral cortex6.93e-5922
neocortex1.35e-5620
cerebral cortex1.06e-5125
pallium1.06e-5125
pre-chordal neural plate3.22e-5161
ecto-epithelium9.70e-49104
structure with developmental contribution from neural crest5.74e-40132
adult organism2.31e-38114
ectoderm-derived structure5.36e-29171
ectoderm5.36e-29171
presumptive ectoderm5.36e-29171
organ system subdivision3.84e-24223
gyrus2.07e-236
brainstem6.91e-236
segmental subdivision of hindbrain3.19e-2212
hindbrain3.19e-2212
presumptive hindbrain3.19e-2212
neural nucleus5.04e-229
nucleus of brain5.04e-229
tube5.51e-22192
segmental subdivision of nervous system1.90e-2013
temporal lobe4.79e-206
occipital lobe4.78e-185
posterior neural tube1.32e-1715
chordal neural plate1.32e-1715
pons2.67e-173
anatomical conduit2.16e-16240
regional part of metencephalon9.43e-169
metencephalon9.43e-169
future metencephalon9.43e-169
organ part9.74e-16218
basal ganglion1.21e-159
nuclear complex of neuraxis1.21e-159
aggregate regional part of brain1.21e-159
collection of basal ganglia1.21e-159
cerebral subcortex1.21e-159
corpus striatum2.49e-134
striatum2.49e-134
ventral part of telencephalon2.49e-134
future corpus striatum2.49e-134
telencephalic nucleus4.18e-137
multi-tissue structure1.09e-12342
epithelium1.26e-12306
middle temporal gyrus1.49e-122
cell layer1.92e-12309
locus ceruleus2.95e-122
brainstem nucleus2.95e-122
hindbrain nucleus2.95e-122
anatomical cluster5.47e-12373
limbic system7.01e-115
parietal lobe1.36e-105
frontal cortex1.06e-083
caudate-putamen1.06e-083
dorsal striatum1.06e-083
medulla oblongata2.91e-083
myelencephalon2.91e-083
future myelencephalon2.91e-083
diencephalon7.74e-087
future diencephalon7.74e-087
olfactory region3.36e-071
primary subdivision of skull3.36e-071
cranium3.36e-071
neurocranium3.36e-071
chondrocranium3.36e-071
cartilaginous neurocranium3.36e-071
head paraxial mesoderm3.36e-071
putamen4.01e-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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