Personal tools

Coexpression cluster:C555: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C555_cerebellum_pineal_occipital_middle_parietal_medial_locus |id=C555 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C555_cerebellum_pineal_occipital_middle_parietal_medial_locus
|full_id=C555_cerebellum_pineal_occipital_middle_parietal_medial_locus
|id=C555
|id=C555
|ontology_enrichment_celltype=CL:0000055!6.26e-09!180
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.91e-43!115;UBERON:0000073!7.11e-40!94;UBERON:0001016!7.11e-40!94;UBERON:0005743!7.46e-38!86;UBERON:0001017!1.04e-36!82;UBERON:0002346!8.52e-35!90;UBERON:0003075!1.16e-34!86;UBERON:0007284!1.16e-34!86;UBERON:0001049!2.65e-34!57;UBERON:0005068!2.65e-34!57;UBERON:0006241!2.65e-34!57;UBERON:0007135!2.65e-34!57;UBERON:0000955!1.44e-31!69;UBERON:0006238!1.44e-31!69;UBERON:0002616!1.56e-31!59;UBERON:0000924!1.70e-29!173;UBERON:0006601!1.70e-29!173;UBERON:0004121!5.66e-29!169;UBERON:0003080!6.01e-26!42;UBERON:0000033!8.29e-26!123;UBERON:0002780!1.62e-25!41;UBERON:0001890!1.62e-25!41;UBERON:0006240!1.62e-25!41;UBERON:0000153!3.57e-25!129;UBERON:0007811!3.57e-25!129;UBERON:0003056!4.16e-25!61;UBERON:0000475!5.52e-24!365;UBERON:0002020!2.90e-21!34;UBERON:0003528!2.90e-21!34;UBERON:0001893!3.48e-21!34;UBERON:0002791!1.45e-20!33;UBERON:0000481!2.97e-20!347;UBERON:0001869!5.01e-20!32;UBERON:0000483!3.83e-19!309;UBERON:0000119!8.52e-19!312;UBERON:0000468!6.68e-18!659;UBERON:0000025!2.05e-16!194;UBERON:0000956!8.20e-16!25;UBERON:0000203!8.20e-16!25;UBERON:0000477!1.35e-15!286;UBERON:0002619!1.85e-15!22;UBERON:0004111!2.15e-15!241;UBERON:0001950!3.01e-14!20;UBERON:0000467!3.18e-13!625;UBERON:0000480!6.79e-13!626;UBERON:0000922!1.96e-12!612;UBERON:0000064!4.42e-11!219;UBERON:0002050!6.63e-11!605;UBERON:0005423!6.63e-11!605;UBERON:0000923!1.35e-10!604;UBERON:0005291!1.35e-10!604;UBERON:0006598!1.35e-10!604;UBERON:0002532!1.35e-10!604;UBERON:0000062!1.99e-10!511;UBERON:0003076!2.18e-09!15;UBERON:0003057!2.18e-09!15;UBERON:0004732!3.54e-08!13;UBERON:0004733!1.30e-07!12;UBERON:0002028!1.30e-07!12;UBERON:0007277!1.30e-07!12;UBERON:0002308!6.48e-07!9;UBERON:0000125!6.48e-07!9;UBERON:0002420!7.68e-07!9;UBERON:0007245!7.68e-07!9;UBERON:0010009!7.68e-07!9;UBERON:0010011!7.68e-07!9;UBERON:0000454!7.68e-07!9
}}
}}

Revision as of 14:54, 21 May 2012


Full id: C555_cerebellum_pineal_occipital_middle_parietal_medial_locus



Phase1 CAGE Peaks

Hg19::chr10:94000992..94001011,-p@chr10:94000992..94001011
-
Hg19::chr14:27067231..27067247,-p1@NOVA1
Hg19::chr15:61521417..61521460,-p2@RORA
Hg19::chr16:325910..325953,-p1@RGS11
Hg19::chr19:49140692..49140709,-p5@DBP
Hg19::chr19:58566699..58566740,-p@chr19:58566699..58566740
-
Hg19::chr1:204329013..204329086,-p1@PLEKHA6
Hg19::chr1:204654494..204654512,-p4@LRRN2
Hg19::chr22:25202173..25202190,+p3@SGSM1
Hg19::chr22:25202232..25202273,+p2@SGSM1
Hg19::chr22:41956977..41957035,+p2@CSDC2
Hg19::chr3:116164195..116164272,-p2@LSAMP
Hg19::chr6:136847393..136847403,-p15@MAP7
Hg19::chr7:79083072..79083082,-p13@MAGI2
Hg19::chr7:79083088..79083161,-p2@MAGI2
Hg19::chr9:136399759..136399803,+p2@ADAMTSL2


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
non-terminally differentiated cell6.26e-09180
Uber Anatomy
Ontology termp-valuen
adult organism2.91e-43115
regional part of nervous system7.11e-4094
nervous system7.11e-4094
central nervous system1.04e-3682
neurectoderm8.52e-3590
neural plate1.16e-3486
presumptive neural plate1.16e-3486
neural tube2.65e-3457
neural rod2.65e-3457
future spinal cord2.65e-3457
neural keel2.65e-3457
brain1.44e-3169
future brain1.44e-3169
regional part of brain1.56e-3159
ectoderm1.70e-29173
presumptive ectoderm1.70e-29173
ectoderm-derived structure5.66e-29169
anterior neural tube6.01e-2642
head8.29e-26123
regional part of forebrain1.62e-2541
forebrain1.62e-2541
future forebrain1.62e-2541
anterior region of body3.57e-25129
craniocervical region3.57e-25129
pre-chordal neural plate4.16e-2561
organism subdivision5.52e-24365
gray matter2.90e-2134
brain grey matter2.90e-2134
telencephalon3.48e-2134
regional part of telencephalon1.45e-2033
multi-tissue structure2.97e-20347
cerebral hemisphere5.01e-2032
epithelium3.83e-19309
cell layer8.52e-19312
multi-cellular organism6.68e-18659
tube2.05e-16194
cerebral cortex8.20e-1625
pallium8.20e-1625
anatomical cluster1.35e-15286
regional part of cerebral cortex1.85e-1522
anatomical conduit2.15e-15241
neocortex3.01e-1420
anatomical system3.18e-13625
anatomical group6.79e-13626
embryo1.96e-12612
organ part4.42e-11219
embryonic structure6.63e-11605
developing anatomical structure6.63e-11605
germ layer1.35e-10604
embryonic tissue1.35e-10604
presumptive structure1.35e-10604
epiblast (generic)1.35e-10604
organ1.99e-10511
posterior neural tube2.18e-0915
chordal neural plate2.18e-0915
segmental subdivision of nervous system3.54e-0813
segmental subdivision of hindbrain1.30e-0712
hindbrain1.30e-0712
presumptive hindbrain1.30e-0712
nucleus of brain6.48e-079
neural nucleus6.48e-079
basal ganglion7.68e-079
nuclear complex of neuraxis7.68e-079
aggregate regional part of brain7.68e-079
collection of basal ganglia7.68e-079
cerebral subcortex7.68e-079


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.