Personal tools

Coexpression cluster:C1646: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|gostat_on_coexpression_clusters=GO:0004385!guanylate kinase activity!0.018129910939371!1740$GO:0019201!nucleotide kinase activity!0.0299614361024918!1740$GO:0016776!phosphotransferase activity, phosphate group as acceptor!0.0299614361024918!1740$GO:0044459!plasma membrane part!0.0299614361024918!27328;1740$GO:0019205!nucleobase, nucleoside, nucleotide kinase activity!0.0299614361024918!1740$GO:0045211!postsynaptic membrane!0.0378242913176896!1740$GO:0044456!synapse part!0.0378242913176896!1740$GO:0007156!homophilic cell adhesion!0.0392454202050833!27328$GO:0005886!plasma membrane!0.0392454202050833!27328;1740
|gostat_on_coexpression_clusters=GO:0004385!guanylate kinase activity!0.018129910939371!1740$GO:0019201!nucleotide kinase activity!0.0299614361024918!1740$GO:0016776!phosphotransferase activity, phosphate group as acceptor!0.0299614361024918!1740$GO:0044459!plasma membrane part!0.0299614361024918!27328;1740$GO:0019205!nucleobase, nucleoside, nucleotide kinase activity!0.0299614361024918!1740$GO:0045211!postsynaptic membrane!0.0378242913176896!1740$GO:0044456!synapse part!0.0378242913176896!1740$GO:0007156!homophilic cell adhesion!0.0392454202050833!27328$GO:0005886!plasma membrane!0.0392454202050833!27328;1740
|id=C1646
|id=C1646
|ontology_enrichment_celltype=CL:0000047!4.91e-08!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.67e-52!115;UBERON:0001017!1.20e-50!82;UBERON:0001049!5.00e-49!57;UBERON:0005068!5.00e-49!57;UBERON:0006241!5.00e-49!57;UBERON:0007135!5.00e-49!57;UBERON:0000073!7.18e-49!94;UBERON:0001016!7.18e-49!94;UBERON:0005743!1.07e-48!86;UBERON:0002346!2.31e-44!90;UBERON:0002616!1.42e-40!59;UBERON:0003075!1.79e-40!86;UBERON:0007284!1.79e-40!86;UBERON:0002780!3.34e-40!41;UBERON:0001890!3.34e-40!41;UBERON:0006240!3.34e-40!41;UBERON:0000955!1.79e-39!69;UBERON:0006238!1.79e-39!69;UBERON:0003080!7.95e-39!42;UBERON:0000924!1.77e-35!173;UBERON:0006601!1.77e-35!173;UBERON:0002020!3.54e-34!34;UBERON:0003528!3.54e-34!34;UBERON:0001893!6.98e-34!34;UBERON:0002791!6.92e-33!33;UBERON:0001869!1.34e-32!32;UBERON:0004121!2.48e-32!169;UBERON:0003056!4.24e-28!61;UBERON:0000956!1.92e-25!25;UBERON:0000203!1.92e-25!25;UBERON:0002619!5.11e-24!22;UBERON:0001950!5.49e-22!20;UBERON:0000153!6.67e-22!129;UBERON:0007811!6.67e-22!129;UBERON:0000033!2.19e-20!123;UBERON:0003076!3.85e-11!15;UBERON:0003057!3.85e-11!15;UBERON:0002420!2.51e-10!9;UBERON:0007245!2.51e-10!9;UBERON:0010009!2.51e-10!9;UBERON:0010011!2.51e-10!9;UBERON:0000454!2.51e-10!9;UBERON:0002308!4.26e-10!9;UBERON:0000125!4.26e-10!9;UBERON:0000025!5.78e-10!194;UBERON:0004732!2.70e-09!13;UBERON:0001871!3.92e-09!7;UBERON:0000064!5.77e-09!219;UBERON:0000922!5.93e-09!612;UBERON:0004733!9.59e-09!12;UBERON:0002028!9.59e-09!12;UBERON:0007277!9.59e-09!12;UBERON:0009663!3.19e-08!7;UBERON:0001894!1.23e-07!7;UBERON:0006222!1.23e-07!7;UBERON:0000200!1.44e-07!6;UBERON:0000468!2.33e-07!659;UBERON:0004111!3.49e-07!241;UBERON:0000483!4.60e-07!309;UBERON:0000349!8.74e-07!5;UBERON:0000119!9.18e-07!312
}}
}}

Revision as of 14:14, 21 May 2012


Full id: C1646_peripheral_occipital_caudate_parietal_putamen_duodenum_temporal



Phase1 CAGE Peaks

Hg19::chr11:83393280..83393295,-p15@DLG2
Hg19::chr11:83393303..83393342,-p8@DLG2
Hg19::chr11:83393429..83393454,-p12@DLG2
Hg19::chr2:133015374..133015390,-p3@ANKRD30BL
Hg19::chrX:91034366..91034380,+p1@PCDH11X


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


GO IDGO nameFDR corrected p-value
GO:0004385guanylate kinase activity0.018129910939371
GO:0019201nucleotide kinase activity0.0299614361024918
GO:0016776phosphotransferase activity, phosphate group as acceptor0.0299614361024918
GO:0044459plasma membrane part0.0299614361024918
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0299614361024918
GO:0045211postsynaptic membrane0.0378242913176896
GO:0044456synapse part0.0378242913176896
GO:0007156homophilic cell adhesion0.0392454202050833
GO:0005886plasma membrane0.0392454202050833



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 cell4.91e-088
Uber Anatomy
Ontology termp-valuen
adult organism5.67e-52115
central nervous system1.20e-5082
neural tube5.00e-4957
neural rod5.00e-4957
future spinal cord5.00e-4957
neural keel5.00e-4957
regional part of nervous system7.18e-4994
nervous system7.18e-4994
neurectoderm2.31e-4490
regional part of brain1.42e-4059
neural plate1.79e-4086
presumptive neural plate1.79e-4086
regional part of forebrain3.34e-4041
forebrain3.34e-4041
future forebrain3.34e-4041
brain1.79e-3969
future brain1.79e-3969
anterior neural tube7.95e-3942
ectoderm1.77e-35173
presumptive ectoderm1.77e-35173
gray matter3.54e-3434
brain grey matter3.54e-3434
telencephalon6.98e-3434
regional part of telencephalon6.92e-3333
cerebral hemisphere1.34e-3232
ectoderm-derived structure2.48e-32169
pre-chordal neural plate4.24e-2861
cerebral cortex1.92e-2525
pallium1.92e-2525
regional part of cerebral cortex5.11e-2422
neocortex5.49e-2220
anterior region of body6.67e-22129
craniocervical region6.67e-22129
head2.19e-20123
posterior neural tube3.85e-1115
chordal neural plate3.85e-1115
basal ganglion2.51e-109
nuclear complex of neuraxis2.51e-109
aggregate regional part of brain2.51e-109
collection of basal ganglia2.51e-109
cerebral subcortex2.51e-109
nucleus of brain4.26e-109
neural nucleus4.26e-109
tube5.78e-10194
segmental subdivision of nervous system2.70e-0913
temporal lobe3.92e-097
organ part5.77e-09219
embryo5.93e-09612
segmental subdivision of hindbrain9.59e-0912
hindbrain9.59e-0912
presumptive hindbrain9.59e-0912
telencephalic nucleus3.19e-087
diencephalon1.23e-077
future diencephalon1.23e-077
gyrus1.44e-076
multi-cellular organism2.33e-07659
anatomical conduit3.49e-07241
epithelium4.60e-07309
limbic system8.74e-075
cell layer9.18e-07312


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.