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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C298_small_optic_substantia_thalamus_diencephalon_globus_occipital
|full_id=C298_small_optic_substantia_thalamus_diencephalon_globus_occipital
|id=C298
|id=C298

Revision as of 15:49, 12 September 2012


Full id: C298_small_optic_substantia_thalamus_diencephalon_globus_occipital



Phase1 CAGE Peaks

Hg19::chr10:71333172..71333186,-p1@NEUROG3
Hg19::chr12:7401767..7401780,+p@chr12:7401767..7401780
+
Hg19::chr13:112626645..112626656,+p@chr13:112626645..112626656
+
Hg19::chr13:112626665..112626679,+p@chr13:112626665..112626679
+
Hg19::chr13:25685542..25685552,+p@chr13:25685542..25685552
+
Hg19::chr15:92459161..92459167,+p@chr15:92459161..92459167
+
Hg19::chr15:92459244..92459268,+p@chr15:92459244..92459268
+
Hg19::chr15:92459275..92459283,+p@chr15:92459275..92459283
+
Hg19::chr15:92459318..92459327,+p@chr15:92459318..92459327
+
Hg19::chr15:92459332..92459338,+p@chr15:92459332..92459338
+
Hg19::chr16:34378161..34378168,+p@chr16:34378161..34378168
+
Hg19::chr16:85617478..85617492,-p@chr16:85617478..85617492
-
Hg19::chr19:38423014..38423072,+p3@SIPA1L3
Hg19::chr1:40367530..40367597,-p1@MYCL1
Hg19::chr1:40367668..40367684,-p2@MYCL1
Hg19::chr1:40367692..40367703,-p3@MYCL1
Hg19::chr20:21378152..21378169,-p1@NKX2-4
Hg19::chr20:22449463..22449467,-p@chr20:22449463..22449467
-
Hg19::chr21:43733727..43733736,-p8@TFF3
Hg19::chr22:27044125..27044132,-p@chr22:27044125..27044132
-
Hg19::chr22:44569007..44569025,+p8@PARVG
Hg19::chr22:44569031..44569036,+p27@PARVG
Hg19::chr22:47425875..47425879,-p@chr22:47425875..47425879
-
Hg19::chr3:140947563..140947577,+p14@ACPL2
Hg19::chr3:180892810..180892816,+p23@SOX2-OT
Hg19::chr3:180892844..180892856,+p13@SOX2-OT
Hg19::chr3:180892861..180892862,+p31@SOX2-OT
Hg19::chr3:180892876..180892890,+p11@SOX2-OT
Hg19::chr3:181414213..181414253,+p@chr3:181414213..181414253
+
Hg19::chr3:181417231..181417239,+p12@SOX2-OT
Hg19::chr3:181417241..181417256,+p3@SOX2-OT
Hg19::chr3:181417264..181417270,+p7@SOX2-OT
Hg19::chr3:181417276..181417285,+p8@SOX2-OT
Hg19::chr3:181417560..181417569,-p@chr3:181417560..181417569
-
Hg19::chr3:181432833..181432842,+p@chr3:181432833..181432842
+
Hg19::chr3:181459149..181459161,+p@chr3:181459149..181459161
+
Hg19::chr3:181459204..181459208,+p@chr3:181459204..181459208
+
Hg19::chr3:19189765..19189793,+p2@KCNH8
Hg19::chr4:163124750..163124764,-p@chr4:163124750..163124764
-
Hg19::chr5:15516888..15516924,+p@chr5:15516888..15516924
+
Hg19::chr8:53163002..53163004,-p@chr8:53163002..53163004
-
Hg19::chr9:117670443..117670445,-p@chr9:117670443..117670445
-


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
neural tube3.62e-2957
neural rod3.62e-2957
future spinal cord3.62e-2957
neural keel3.62e-2957
adult organism5.42e-29115
central nervous system3.53e-2782
regional part of nervous system1.05e-2694
nervous system1.05e-2694
regional part of forebrain1.35e-2341
forebrain1.35e-2341
future forebrain1.35e-2341
anterior neural tube1.43e-2242
regional part of brain2.32e-2259
neural plate1.38e-2186
presumptive neural plate1.38e-2186
gray matter5.01e-2134
brain grey matter5.01e-2134
telencephalon5.65e-2134
brain6.88e-2169
future brain6.88e-2169
neurectoderm1.62e-2090
regional part of telencephalon2.08e-2033
cerebral hemisphere1.21e-1932
embryo4.86e-19612
embryonic structure9.96e-17605
developing anatomical structure9.96e-17605
germ layer1.59e-16604
embryonic tissue1.59e-16604
presumptive structure1.59e-16604
epiblast (generic)1.59e-16604
pre-chordal neural plate3.79e-1661
cerebral cortex1.96e-1525
pallium1.96e-1525
ectoderm-derived structure5.40e-15169
regional part of cerebral cortex6.38e-1522
ectoderm1.40e-14173
presumptive ectoderm1.40e-14173
anatomical group1.53e-14626
anatomical system2.11e-14625
organ6.99e-14511
multi-cellular organism1.03e-13659
neocortex1.14e-1320
head7.33e-13123
anterior region of body1.18e-12129
craniocervical region1.18e-12129
hematopoietic system1.37e-08102
blood island1.37e-08102
posterior neural tube9.44e-0815
chordal neural plate9.44e-0815
bone marrow2.01e-0780
nucleus of brain4.54e-079
neural nucleus4.54e-079
basal ganglion5.58e-079
nuclear complex of neuraxis5.58e-079
aggregate regional part of brain5.58e-079
collection of basal ganglia5.58e-079
cerebral subcortex5.58e-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

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