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Difference between revisions of "Coexpression cluster:C3840"

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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C3840_optic_cerebellum_Neutrophils_Eosinophils_occipital_skeletal_substantia
 
|full_id=C3840_optic_cerebellum_Neutrophils_Eosinophils_occipital_skeletal_substantia
 
|gostat_on_coexpression_clusters=GO:0008089!anterograde axon cargo transport!0.00476863299187566!23095$GO:0008088!axon cargo transport!0.00476863299187566!23095$GO:0019894!kinesin binding!0.00476863299187566!23095$GO:0007274!neuromuscular synaptic transmission!0.00476863299187566!23095$GO:0007270!nerve-nerve synaptic transmission!0.00805369127516778!23095$GO:0030659!cytoplasmic vesicle membrane!0.029936418226775!23095$GO:0044433!cytoplasmic vesicle part!0.029936418226775!23095$GO:0012506!vesicle membrane!0.029936418226775!23095$GO:0003777!microtubule motor activity!0.0332038149063935!23095$GO:0007018!microtubule-based movement!0.0346167432002826!23095$GO:0005875!microtubule associated complex!0.0346167432002826!23095$GO:0030705!cytoskeleton-dependent intracellular transport!0.0346167432002826!23095$GO:0007268!synaptic transmission!0.0414458966207465!23095$GO:0005874!microtubule!0.0414458966207465!23095$GO:0007017!microtubule-based process!0.0414458966207465!23095$GO:0019226!transmission of nerve impulse!0.0414458966207465!23095$GO:0016023!cytoplasmic membrane-bound vesicle!0.0414458966207465!23095$GO:0031988!membrane-bound vesicle!0.0414458966207465!23095$GO:0031410!cytoplasmic vesicle!0.0457788767220064!23095$GO:0031982!vesicle!0.0457788767220064!23095
 
|gostat_on_coexpression_clusters=GO:0008089!anterograde axon cargo transport!0.00476863299187566!23095$GO:0008088!axon cargo transport!0.00476863299187566!23095$GO:0019894!kinesin binding!0.00476863299187566!23095$GO:0007274!neuromuscular synaptic transmission!0.00476863299187566!23095$GO:0007270!nerve-nerve synaptic transmission!0.00805369127516778!23095$GO:0030659!cytoplasmic vesicle membrane!0.029936418226775!23095$GO:0044433!cytoplasmic vesicle part!0.029936418226775!23095$GO:0012506!vesicle membrane!0.029936418226775!23095$GO:0003777!microtubule motor activity!0.0332038149063935!23095$GO:0007018!microtubule-based movement!0.0346167432002826!23095$GO:0005875!microtubule associated complex!0.0346167432002826!23095$GO:0030705!cytoskeleton-dependent intracellular transport!0.0346167432002826!23095$GO:0007268!synaptic transmission!0.0414458966207465!23095$GO:0005874!microtubule!0.0414458966207465!23095$GO:0007017!microtubule-based process!0.0414458966207465!23095$GO:0019226!transmission of nerve impulse!0.0414458966207465!23095$GO:0016023!cytoplasmic membrane-bound vesicle!0.0414458966207465!23095$GO:0031988!membrane-bound vesicle!0.0414458966207465!23095$GO:0031410!cytoplasmic vesicle!0.0457788767220064!23095$GO:0031982!vesicle!0.0457788767220064!23095

Revision as of 07:49, 12 September 2012


Full id: C3840_optic_cerebellum_Neutrophils_Eosinophils_occipital_skeletal_substantia



Phase1 CAGE Peaks

  Short description
Hg19::chr1:10270620..10270637,+ p1@KIF1B
Hg19::chr1:10270675..10270686,+ p5@KIF1B
Hg19::chr5:147763388..147763474,- p1@ENST00000501695
p1@uc003lpb.1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0008089anterograde axon cargo transport0.00476863299187566
GO:0008088axon cargo transport0.00476863299187566
GO:0019894kinesin binding0.00476863299187566
GO:0007274neuromuscular synaptic transmission0.00476863299187566
GO:0007270nerve-nerve synaptic transmission0.00805369127516778
GO:0030659cytoplasmic vesicle membrane0.029936418226775
GO:0044433cytoplasmic vesicle part0.029936418226775
GO:0012506vesicle membrane0.029936418226775
GO:0003777microtubule motor activity0.0332038149063935
GO:0007018microtubule-based movement0.0346167432002826
GO:0005875microtubule associated complex0.0346167432002826
GO:0030705cytoskeleton-dependent intracellular transport0.0346167432002826
GO:0007268synaptic transmission0.0414458966207465
GO:0005874microtubule0.0414458966207465
GO:0007017microtubule-based process0.0414458966207465
GO:0019226transmission of nerve impulse0.0414458966207465
GO:0016023cytoplasmic membrane-bound vesicle0.0414458966207465
GO:0031988membrane-bound vesicle0.0414458966207465
GO:0031410cytoplasmic vesicle0.0457788767220064
GO:0031982vesicle0.0457788767220064



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism1.40e-35115
central nervous system6.76e-3282
neural tube1.07e-3057
neural rod1.07e-3057
future spinal cord1.07e-3057
neural keel1.07e-3057
multi-cellular organism7.28e-29659
anatomical system9.39e-29625
anatomical group1.03e-28626
brain3.13e-2869
future brain3.13e-2869
regional part of nervous system5.89e-2894
nervous system5.89e-2894
regional part of brain1.18e-2759
anterior neural tube1.74e-2442
regional part of forebrain3.38e-2441
forebrain3.38e-2441
future forebrain3.38e-2441
organ4.93e-24511
neural plate1.37e-2386
presumptive neural plate1.37e-2386
embryo3.85e-23612
embryonic structure3.68e-22605
developing anatomical structure3.68e-22605
germ layer9.81e-22604
embryonic tissue9.81e-22604
presumptive structure9.81e-22604
epiblast (generic)9.81e-22604
head1.53e-21123
neurectoderm2.03e-2190
telencephalon1.33e-2034
gray matter1.46e-2034
brain grey matter1.46e-2034
regional part of telencephalon5.57e-2033
anterior region of body9.09e-20129
craniocervical region9.09e-20129
ectoderm-derived structure2.13e-19169
cerebral hemisphere3.00e-1932
ectoderm3.53e-18173
presumptive ectoderm3.53e-18173
pre-chordal neural plate1.40e-1661
cerebral cortex3.11e-1525
pallium3.11e-1525
regional part of cerebral cortex2.66e-1422
neocortex4.39e-1320
skeletal element4.99e-11101
skeletal system4.99e-11101
anatomical conduit9.46e-11241
bone element1.86e-1086
bone marrow1.41e-0980
tube1.48e-09194
anatomical cluster1.14e-08286
organism subdivision7.85e-08365
posterior neural tube1.99e-0715
chordal neural plate1.99e-0715
musculoskeletal system5.53e-07167
epithelium5.66e-07309
cell layer7.97e-07312
nucleus of brain8.48e-079
neural nucleus8.48e-079


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066435.360256373075030.0064925092527670.0279467161459726
CTCFL#140690319.74647435897440.0001298372005551160.00171755128420213
E2F1#186934.907389214879320.008460985347239390.0325412207210582
E2F6#187635.017155731697390.00791769806886330.0322233835482041
ELF1#199734.258097958807540.01295179875054610.0462357434272725
FOS#235338.99795530889440.001372499272417130.00897573271834518
GABPB1#255337.067683836182170.002832212825417420.0154123319754987
IRF1#365937.63716375356390.002244692747297240.0128091719940431
IRF3#3661231.32130147432640.001339514673320110.00887731283500726
MYC#460935.22228187160940.007020843755740150.0294537015868948
NANOG#79923219.49651898734180.003427255648501020.0174468294342853
NFKB1#479035.488063424193840.006049381815655430.0269639105221816
NFYA#4800212.28372046655370.008516011403724430.0324789554116848
NFYB#4801211.17319550235760.01025467135054530.0381351524419455
PAX5#507936.669565531177830.003370290999677260.0172925483525077
PBX3#5090214.60967512449610.006056122473217890.0268359020314991
RAD21#5885310.35503389545630.0009004912073565420.00664075704032692
SIN3A#2594235.408884726815140.006318961977991520.0276788185219753
SMARCB1#6598212.16847718743830.008675002221921740.0329889512472795
SMC3#9126210.02995522995520.0126656379767470.0457474170725741
SP2#6668217.43568699589640.004273568481769740.0203199280067175
TAF7#6879311.43306940492390.0006690181981945830.00543113809570494
YY1#752834.911170749853860.008441455341808260.0329416416112959
ZBTB7A#5134137.35190930787590.002516255860282270.0140202329167744
ZNF263#1012738.221841637010680.001799043925565870.0109416694934879



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.