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Coexpression cluster:C1084: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!2.12e-75!56;UBERON:0005068!2.12e-75!56;UBERON:0006241!2.12e-75!56;UBERON:0007135!2.12e-75!56;UBERON:0001017!7.24e-69!81;UBERON:0000073!8.61e-68!53;UBERON:0002616!8.61e-68!53;UBERON:0001016!6.98e-61!89;UBERON:0000955!1.65e-55!68;UBERON:0006238!1.65e-55!68;UBERON:0003528!5.66e-53!34;UBERON:0002020!5.66e-53!34;UBERON:0001893!1.82e-52!34;UBERON:0003075!9.96e-51!82;UBERON:0007284!9.96e-51!82;UBERON:0002346!2.53e-50!86;UBERON:0002780!1.15e-49!41;UBERON:0001890!1.15e-49!41;UBERON:0003080!1.15e-49!41;UBERON:0006240!1.15e-49!41;UBERON:0002791!7.13e-48!32;UBERON:0001869!1.26e-47!32;UBERON:0010371!1.01e-39!104;UBERON:0002619!2.03e-35!22;UBERON:0001950!1.22e-34!20;UBERON:0003056!2.82e-33!61;UBERON:0007023!5.82e-33!114;UBERON:0000956!9.18e-31!25;UBERON:0000203!9.18e-31!25;UBERON:0004121!2.10e-30!171;UBERON:0000924!2.10e-30!171;UBERON:0006601!2.10e-30!171;UBERON:0010314!4.76e-29!132;UBERON:0003076!2.71e-26!15;UBERON:0003057!2.71e-26!15;UBERON:0000125!1.82e-25!9;UBERON:0002308!1.82e-25!9;UBERON:0011216!5.73e-23!223;UBERON:0009663!3.72e-20!7;UBERON:0002420!3.93e-20!9;UBERON:0007245!3.93e-20!9;UBERON:0010009!3.93e-20!9;UBERON:0010011!3.93e-20!9;UBERON:0000454!3.93e-20!9;UBERON:0004733!8.72e-19!12;UBERON:0002028!8.72e-19!12;UBERON:0007277!8.72e-19!12;UBERON:0000025!1.31e-17!192;UBERON:0004732!3.41e-17!13;UBERON:0002298!6.26e-17!6;UBERON:0001872!4.33e-14!5;UBERON:0000369!1.99e-12!4;UBERON:0002435!1.99e-12!4;UBERON:0000204!1.99e-12!4;UBERON:0010082!1.99e-12!4;UBERON:0004111!6.56e-12!240;UBERON:0002680!8.13e-12!9;UBERON:0001895!8.13e-12!9;UBERON:0010092!8.13e-12!9;UBERON:0000200!2.19e-11!6;UBERON:0000477!1.54e-10!373;UBERON:0000064!5.88e-10!218;UBERON:0001871!6.40e-10!6;UBERON:0005383!6.71e-10!3;UBERON:0005382!6.71e-10!3;UBERON:0002240!1.27e-09!3;UBERON:0005174!1.27e-09!3;UBERON:0001137!1.27e-09!3;UBERON:0000988!2.33e-09!3;UBERON:0002021!2.44e-09!5;UBERON:0001896!2.84e-09!3;UBERON:0005290!2.84e-09!3;UBERON:0010096!2.84e-09!3;UBERON:0000483!7.12e-09!306;UBERON:0000119!1.11e-08!309;UBERON:0000922!1.07e-07!592;UBERON:0001873!4.61e-07!2;UBERON:0010122!4.61e-07!2;UBERON:0002148!5.34e-07!2;UBERON:0006331!5.34e-07!2;UBERON:0009662!5.34e-07!2
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,0.481684,0.301904,1.20684,0.554663,0.561282,0.190005,0.154405,0.450635,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.0766963,0.341703,0.405031,0.472508,0.29709,0.385586,0.619829,0.135503,0.470396,0.304828,0.122648,0.429397,0.810962,0.220667,0.469827,0.269459,0.0137136,0.266487,0.481208,0.244807,0.518171,0.268162,0.413601,0.0547276,1.47072,0.0169887,0.371118,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.0927889,0.887323,1.03948,0.546236,0.831988,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,0.63188,1.03748,0.149081,0.138565,0.401476,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,0.0220225,0.0757344,0.378318,0.659621,1.59442,1.22073,0.959334,1.93366,0.227232,0.817658,0.672575,0.162291,0.87,0.664183,0.106284,0.246049,1.92212,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,1.77423,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.732093,0.0278613,0.428232,0.710479,0.650514,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.735874,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,0.0510299,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.00340764
}}
}}

Revision as of 14:40, 26 November 2012


Full id: C1084_cerebellum_iPS_HES3GFP_nonsmall_occipital_parietal_caudate



Phase1 CAGE Peaks

Hg19::chr4:93224865..93224903,+p@chr4:93224865..93224903
+
Hg19::chr4:93224904..93224918,+p@chr4:93224904..93224918
+
Hg19::chr4:93329615..93329616,+p@chr4:93329615..93329616
+
Hg19::chr4:93520199..93520202,+p@chr4:93520199..93520202
+
Hg19::chr4:93587821..93587823,+p@chr4:93587821..93587823
+
Hg19::chr4:93706240..93706244,+p@chr4:93706240..93706244
+
Hg19::chr4:93851749..93851753,+p@chr4:93851749..93851753
+
Hg19::chr4:94044063..94044065,+p@chr4:94044063..94044065
+


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>

Cell Type
Ontology termp-valuen
embryonic stem cell1.46e-135
neuron1.51e-086
neuroblast1.51e-086
electrically signaling cell1.51e-086
Uber Anatomy
Ontology termp-valuen
neural tube2.12e-7556
neural rod2.12e-7556
future spinal cord2.12e-7556
neural keel2.12e-7556
central nervous system7.24e-6981
regional part of nervous system8.61e-6853
regional part of brain8.61e-6853
nervous system6.98e-6189
brain1.65e-5568
future brain1.65e-5568
brain grey matter5.66e-5334
gray matter5.66e-5334
telencephalon1.82e-5234
neural plate9.96e-5182
presumptive neural plate9.96e-5182
neurectoderm2.53e-5086
regional part of forebrain1.15e-4941
forebrain1.15e-4941
anterior neural tube1.15e-4941
future forebrain1.15e-4941
regional part of telencephalon7.13e-4832
cerebral hemisphere1.26e-4732
ecto-epithelium1.01e-39104
regional part of cerebral cortex2.03e-3522
neocortex1.22e-3420
pre-chordal neural plate2.82e-3361
adult organism5.82e-33114
cerebral cortex9.18e-3125
pallium9.18e-3125
ectoderm-derived structure2.10e-30171
ectoderm2.10e-30171
presumptive ectoderm2.10e-30171
structure with developmental contribution from neural crest4.76e-29132
posterior neural tube2.71e-2615
chordal neural plate2.71e-2615
neural nucleus1.82e-259
nucleus of brain1.82e-259
organ system subdivision5.73e-23223
telencephalic nucleus3.72e-207
basal ganglion3.93e-209
nuclear complex of neuraxis3.93e-209
aggregate regional part of brain3.93e-209
collection of basal ganglia3.93e-209
cerebral subcortex3.93e-209
segmental subdivision of hindbrain8.72e-1912
hindbrain8.72e-1912
presumptive hindbrain8.72e-1912
tube1.31e-17192
segmental subdivision of nervous system3.41e-1713
brainstem6.26e-176
parietal lobe4.33e-145
corpus striatum1.99e-124
striatum1.99e-124
ventral part of telencephalon1.99e-124
future corpus striatum1.99e-124
anatomical conduit6.56e-12240
regional part of metencephalon8.13e-129
metencephalon8.13e-129
future metencephalon8.13e-129
gyrus2.19e-116
anatomical cluster1.54e-10373
organ part5.88e-10218
temporal lobe6.40e-106
caudate-putamen6.71e-103
dorsal striatum6.71e-103
spinal cord1.27e-093
dorsal region element1.27e-093
dorsum1.27e-093
pons2.33e-093
occipital lobe2.44e-095
medulla oblongata2.84e-093
myelencephalon2.84e-093
future myelencephalon2.84e-093
epithelium7.12e-09306
cell layer1.11e-08309
embryo1.07e-07592
caudate nucleus4.61e-072
future caudate nucleus4.61e-072
locus ceruleus5.34e-072
brainstem nucleus5.34e-072
hindbrain nucleus5.34e-072


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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