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Coexpression cluster:C3840

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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 organism1.51e-35114
central nervous system2.92e-3181
neural tube9.01e-3056
neural rod9.01e-3056
future spinal cord9.01e-3056
neural keel9.01e-3056
nervous system4.91e-2989
regional part of nervous system6.08e-2853
regional part of brain6.08e-2853
brain3.82e-2768
future brain3.82e-2768
multi-cellular organism2.69e-26656
anatomical system4.02e-26624
anatomical group6.66e-26625
regional part of forebrain4.46e-2441
forebrain4.46e-2441
anterior neural tube4.46e-2441
future forebrain4.46e-2441
neural plate1.30e-2282
presumptive neural plate1.30e-2282
embryonic structure5.19e-21564
neurectoderm8.63e-2186
telencephalon1.95e-2034
brain grey matter2.21e-2034
gray matter2.21e-2034
germ layer2.25e-20560
germ layer / neural crest2.25e-20560
embryonic tissue2.25e-20560
presumptive structure2.25e-20560
germ layer / neural crest derived structure2.25e-20560
epiblast (generic)2.25e-20560
structure with developmental contribution from neural crest2.36e-20132
developing anatomical structure3.49e-20581
organ1.08e-19503
embryo1.55e-19592
regional part of telencephalon3.64e-1932
cerebral hemisphere4.44e-1932
ectoderm-derived structure1.70e-17171
ectoderm1.70e-17171
presumptive ectoderm1.70e-17171
pre-chordal neural plate1.43e-1661
organ system subdivision8.01e-16223
ecto-epithelium8.94e-16104
cerebral cortex5.13e-1525
pallium5.13e-1525
regional part of cerebral cortex5.47e-1422
neocortex8.25e-1320
anatomical cluster8.06e-12373
skeletal system1.03e-10100
bone element1.29e-1082
anatomical conduit7.31e-10240
bone marrow1.33e-0976
skeletal element1.91e-0990
tube5.76e-09192
immune system1.04e-0793
multi-tissue structure1.13e-07342
tissue4.70e-07773
hemolymphoid system4.78e-07108
posterior neural tube5.34e-0715
chordal neural plate5.34e-0715
hematopoietic system5.67e-0798
blood island5.67e-0798
basal ganglion7.22e-079
nuclear complex of neuraxis7.22e-079
aggregate regional part of brain7.22e-079
collection of basal ganglia7.22e-079
cerebral subcortex7.22e-079
neural nucleus7.65e-079
nucleus of brain7.65e-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.