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Coexpression cluster:C1503: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.37e-59!115;UBERON:0001017!3.99e-49!82;UBERON:0001049!7.01e-48!57;UBERON:0005068!7.01e-48!57;UBERON:0006241!7.01e-48!57;UBERON:0007135!7.01e-48!57;UBERON:0005743!1.10e-47!86;UBERON:0002346!5.40e-47!90;UBERON:0000073!2.30e-46!94;UBERON:0001016!2.30e-46!94;UBERON:0003075!3.81e-42!86;UBERON:0007284!3.81e-42!86;UBERON:0002616!2.06e-39!59;UBERON:0000955!1.24e-37!69;UBERON:0006238!1.24e-37!69;UBERON:0002780!5.93e-36!41;UBERON:0001890!5.93e-36!41;UBERON:0006240!5.93e-36!41;UBERON:0000924!7.63e-35!173;UBERON:0006601!7.63e-35!173;UBERON:0003080!8.42e-35!42;UBERON:0001893!6.78e-33!34;UBERON:0002020!8.38e-33!34;UBERON:0003528!8.38e-33!34;UBERON:0002791!1.36e-31!33;UBERON:0004121!3.77e-31!169;UBERON:0001869!7.96e-31!32;UBERON:0003056!4.93e-28!61;UBERON:0002619!4.99e-27!22;UBERON:0000153!5.70e-26!129;UBERON:0007811!5.70e-26!129;UBERON:0000033!6.45e-25!123;UBERON:0001950!2.55e-24!20;UBERON:0000956!5.80e-23!25;UBERON:0000203!5.80e-23!25;UBERON:0003076!8.10e-14!15;UBERON:0003057!8.10e-14!15;UBERON:0000025!2.10e-13!194;UBERON:0000468!7.93e-13!659;UBERON:0000064!1.13e-12!219;UBERON:0000477!1.84e-12!286;UBERON:0004111!4.22e-12!241;UBERON:0004732!8.13e-12!13;UBERON:0002420!1.19e-11!9;UBERON:0007245!1.19e-11!9;UBERON:0010009!1.19e-11!9;UBERON:0010011!1.19e-11!9;UBERON:0000454!1.19e-11!9;UBERON:0000062!1.84e-11!511;UBERON:0002308!2.51e-11!9;UBERON:0000125!2.51e-11!9;UBERON:0000922!3.65e-11!612;UBERON:0000483!3.75e-11!309;UBERON:0000119!8.03e-11!312;UBERON:0004733!9.92e-11!12;UBERON:0002028!9.92e-11!12;UBERON:0007277!9.92e-11!12;UBERON:0000923!3.03e-10!604;UBERON:0005291!3.03e-10!604;UBERON:0006598!3.03e-10!604;UBERON:0002532!3.03e-10!604;UBERON:0002050!3.63e-10!605;UBERON:0005423!3.63e-10!605;UBERON:0000475!3.90e-10!365;UBERON:0000481!6.24e-10!347;UBERON:0000467!6.54e-10!625;UBERON:0000480!7.81e-10!626;UBERON:0002680!1.33e-09!9;UBERON:0001895!1.33e-09!9;UBERON:0010092!1.33e-09!9;UBERON:0009663!5.63e-09!7;UBERON:0001871!7.90e-09!7;UBERON:0000200!8.09e-09!6;UBERON:0000349!2.59e-08!5;UBERON:0001872!1.28e-07!5;UBERON:0002021!2.16e-07!5
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}}
}}

Revision as of 17:22, 8 August 2012


Full id: C1503_cerebellum_heart_small_left_hippocampus_skeletal_occipital



Phase1 CAGE Peaks

Hg19::chr2:229046330..229046346,-p4@SPHKAP
Hg19::chr2:229046362..229046373,-p6@SPHKAP
Hg19::chr2:229046385..229046408,-p1@SPHKAP
Hg19::chr2:229046419..229046438,-p2@SPHKAP
Hg19::chr2:229046447..229046465,-p3@SPHKAP
Hg19::chr2:229046721..229046736,-p7@SPHKAP


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
neuronal stem cell3.01e-078
Uber Anatomy
Ontology termp-valuen
adult organism9.37e-59115
central nervous system3.99e-4982
neural tube7.01e-4857
neural rod7.01e-4857
future spinal cord7.01e-4857
neural keel7.01e-4857
neurectoderm5.40e-4790
regional part of nervous system2.30e-4694
nervous system2.30e-4694
neural plate3.81e-4286
presumptive neural plate3.81e-4286
regional part of brain2.06e-3959
brain1.24e-3769
future brain1.24e-3769
regional part of forebrain5.93e-3641
forebrain5.93e-3641
future forebrain5.93e-3641
ectoderm7.63e-35173
presumptive ectoderm7.63e-35173
anterior neural tube8.42e-3542
telencephalon6.78e-3334
gray matter8.38e-3334
brain grey matter8.38e-3334
regional part of telencephalon1.36e-3133
ectoderm-derived structure3.77e-31169
cerebral hemisphere7.96e-3132
pre-chordal neural plate4.93e-2861
regional part of cerebral cortex4.99e-2722
anterior region of body5.70e-26129
craniocervical region5.70e-26129
head6.45e-25123
neocortex2.55e-2420
cerebral cortex5.80e-2325
pallium5.80e-2325
posterior neural tube8.10e-1415
chordal neural plate8.10e-1415
tube2.10e-13194
multi-cellular organism7.93e-13659
organ part1.13e-12219
anatomical cluster1.84e-12286
anatomical conduit4.22e-12241
segmental subdivision of nervous system8.13e-1213
basal ganglion1.19e-119
nuclear complex of neuraxis1.19e-119
aggregate regional part of brain1.19e-119
collection of basal ganglia1.19e-119
cerebral subcortex1.19e-119
organ1.84e-11511
nucleus of brain2.51e-119
neural nucleus2.51e-119
embryo3.65e-11612
epithelium3.75e-11309
cell layer8.03e-11312
segmental subdivision of hindbrain9.92e-1112
hindbrain9.92e-1112
presumptive hindbrain9.92e-1112
germ layer3.03e-10604
embryonic tissue3.03e-10604
presumptive structure3.03e-10604
epiblast (generic)3.03e-10604
embryonic structure3.63e-10605
developing anatomical structure3.63e-10605
organism subdivision3.90e-10365
multi-tissue structure6.24e-10347
anatomical system6.54e-10625
anatomical group7.81e-10626
regional part of metencephalon1.33e-099
metencephalon1.33e-099
future metencephalon1.33e-099
telencephalic nucleus5.63e-097
temporal lobe7.90e-097
gyrus8.09e-096
limbic system2.59e-085
parietal lobe1.28e-075
occipital lobe2.16e-075


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.