Personal tools

Coexpression cluster:C1233: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C1233_cerebellum_occipital_medial_parietal_amygdala_hippocampus_caudate |id=C1233 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C1233_cerebellum_occipital_medial_parietal_amygdala_hippocampus_caudate
|full_id=C1233_cerebellum_occipital_medial_parietal_amygdala_hippocampus_caudate
|id=C1233
|id=C1233
|ontology_enrichment_celltype=CL:0002319!5.55e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.25e-46!82;UBERON:0001049!5.43e-46!57;UBERON:0005068!5.43e-46!57;UBERON:0006241!5.43e-46!57;UBERON:0007135!5.43e-46!57;UBERON:0000073!7.65e-46!94;UBERON:0001016!7.65e-46!94;UBERON:0005743!1.08e-44!86;UBERON:0000955!5.79e-38!69;UBERON:0006238!5.79e-38!69;UBERON:0002780!8.26e-38!41;UBERON:0001890!8.26e-38!41;UBERON:0006240!8.26e-38!41;UBERON:0002616!1.09e-37!59;UBERON:0002346!6.27e-37!90;UBERON:0003080!1.77e-36!42;UBERON:0003075!9.24e-36!86;UBERON:0007284!9.24e-36!86;UBERON:0002020!6.69e-34!34;UBERON:0003528!6.69e-34!34;UBERON:0001893!1.35e-33!34;UBERON:0002791!1.10e-32!33;UBERON:0001869!5.20e-32!32;UBERON:0000924!5.17e-28!173;UBERON:0006601!5.17e-28!173;UBERON:0007023!5.90e-28!115;UBERON:0003056!7.57e-27!61;UBERON:0004121!8.46e-27!169;UBERON:0000956!2.01e-25!25;UBERON:0000203!2.01e-25!25;UBERON:0002619!1.27e-23!22;UBERON:0001950!1.31e-21!20;UBERON:0000033!8.32e-21!123;UBERON:0000153!2.02e-19!129;UBERON:0007811!2.02e-19!129;UBERON:0003076!1.66e-10!15;UBERON:0003057!1.66e-10!15;UBERON:0002420!5.62e-10!9;UBERON:0007245!5.62e-10!9;UBERON:0010009!5.62e-10!9;UBERON:0010011!5.62e-10!9;UBERON:0000454!5.62e-10!9;UBERON:0002308!7.69e-10!9;UBERON:0000125!7.69e-10!9;UBERON:0001871!4.87e-09!7;UBERON:0004732!8.63e-09!13;UBERON:0004733!4.68e-08!12;UBERON:0002028!4.68e-08!12;UBERON:0007277!4.68e-08!12;UBERON:0009663!5.74e-08!7;UBERON:0000025!5.82e-08!194;UBERON:0000200!2.07e-07!6;UBERON:0000064!7.73e-07!219
}}
}}

Revision as of 14:08, 21 May 2012


Full id: C1233_cerebellum_occipital_medial_parietal_amygdala_hippocampus_caudate



Phase1 CAGE Peaks

Hg19::chr17:7559761..7559772,+p14@ATP1B2
Hg19::chr20:10287270..10287295,+p@chr20:10287270..10287295
+
Hg19::chr2:149868148..149868166,+p@chr2:149868148..149868166
+
Hg19::chr3:121086468..121086472,+p@chr3:121086468..121086472
+
Hg19::chr5:161277593..161277604,-p@chr5:161277593..161277604
-
Hg19::chr5:36687531..36687542,+p@chr5:36687531..36687542
+
Hg19::chr6:31512638..31512648,-p@chr6:31512638..31512648
-


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
neural cell5.55e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system1.25e-4682
neural tube5.43e-4657
neural rod5.43e-4657
future spinal cord5.43e-4657
neural keel5.43e-4657
regional part of nervous system7.65e-4694
nervous system7.65e-4694
brain5.79e-3869
future brain5.79e-3869
regional part of forebrain8.26e-3841
forebrain8.26e-3841
future forebrain8.26e-3841
regional part of brain1.09e-3759
neurectoderm6.27e-3790
anterior neural tube1.77e-3642
neural plate9.24e-3686
presumptive neural plate9.24e-3686
gray matter6.69e-3434
brain grey matter6.69e-3434
telencephalon1.35e-3334
regional part of telencephalon1.10e-3233
cerebral hemisphere5.20e-3232
ectoderm5.17e-28173
presumptive ectoderm5.17e-28173
adult organism5.90e-28115
pre-chordal neural plate7.57e-2761
ectoderm-derived structure8.46e-27169
cerebral cortex2.01e-2525
pallium2.01e-2525
regional part of cerebral cortex1.27e-2322
neocortex1.31e-2120
head8.32e-21123
anterior region of body2.02e-19129
craniocervical region2.02e-19129
posterior neural tube1.66e-1015
chordal neural plate1.66e-1015
basal ganglion5.62e-109
nuclear complex of neuraxis5.62e-109
aggregate regional part of brain5.62e-109
collection of basal ganglia5.62e-109
cerebral subcortex5.62e-109
nucleus of brain7.69e-109
neural nucleus7.69e-109
temporal lobe4.87e-097
segmental subdivision of nervous system8.63e-0913
segmental subdivision of hindbrain4.68e-0812
hindbrain4.68e-0812
presumptive hindbrain4.68e-0812
telencephalic nucleus5.74e-087
tube5.82e-08194
gyrus2.07e-076
organ part7.73e-07219


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.