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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0.0506760246065907,0,0,0,0,0,0.340541246591825,0.080626736260243,0.448966875927917,0.943370045370155,0.502184397184757,0.521392545422672,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0861021576689585,0.36469768556807,0.190433856849312,0.170977399169312,0.304236634647437,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.275076212240664,0.197604689528463,0.0457141349109768,0,0,0,0,0,0,0,0.0251578387782166,0,0,0,0,0,0,0.0740953173184329,0,0.0790270198996655,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.234156469502251,0.255929063729219,0.399763903021909,0.645382896629364,0.288892714678573,0.2281476972156,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0984436487802371,0,0,0,0,0,0,0,0.745106086295706,0.0482120461578062,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.046155979559586,0,0.0431825597942761,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0466451378069441,0,0,0,0,0,0,0,0,0,1.49930850652833,0.89876274699698,0.865341131089426,0.804689727888962,0.725467759001213,0,0,0,0.025130215685849,0,0,0,0,0,0,0,0,0,0,0,0,0.110587055989216,0.655043245752176,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0161109439295801,0,0,0.0217895143979911,0,0,0,0,0,0,0,0,0,0,0,0.099145253918139,0,0,0,0,0,0,0,0,0.0584204843433135,0,0,0,0.0221562293162451,0.0588118185728318,0.0177602205939906,0.0370406554214911,0,0,0,0,0,0,0,0,0,0,0,0,0,0.059690542781635,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0287199675136495,0,0,0,0,0,0.109516364878429,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.05699798491772,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.101234535406224,0,0.600149562354411,0.75722528750091,0,0,0,0.145661221236375,0,0,0.0422874684771159,0,0,0,0,0,0.078198198554358,0,0,0.617529134712306,0.784388752129745,0.587430196947305,0,0,0,0,0,0,0,0,0.0695293501927681,0.757341690818451,0.685330802442937,0.402401944384513,0.491226303129103,0.563472609518775,0.645812292460279,0,0,0.0867837120148719,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0368115019473605,0,0,0,0,1.02433361089128,0,0.927747319466752,0,0.0388046890849592,0,0.0722224018548135,0.344374029099016,0.681604932239042,0.0516822929650548,0,0,0,0,0,0,0,0,0,0,0,0.17131071705705,0,0,0,0,0.0402022792589852,0,0.730542201745058,0,0,0.590544253920471,0,0,0,0,0,0,0,0,0,0,0,0,0,0.055118134803774,0.713337766343257,0.719120562808027,0,0.134701697729745,0,0.149845644847393,0.0896085685791025,0,0,0,0,0.091556269699426,0,0,0,0,0,0,0,0.529647071424384,0.906645702224883,0.188624685641857,0.189125498885892,0.175735909953086,0,0,0.557004031076975,0,0.100548554225161,0.32422518866615,0,0,0.0705414326376335,0.11709348206417,0,0,0,0,0,0,0,0.152925811482126,0,0,0,0.819426158634311,0.712875313968769,0,0,0.0220321056448849,0.143261993003209,0,0,0,0,0,0,0,0,0,0,0.563267984373557,0.626383864900241,0.688212197691363,0.828279042569129,0.815883134348673,0.884812415619612,0,0.0511449590802371,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.031340424028527,0,0,0,0,0,0,0,0.0221543296816198,0,0,0,0,0,0,0,0,0.0483033789388295,0,0.0452211708913631,0,0,0,0,0,0,0,0,0,0,0.620567541081305,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0755925074445696,0.0222355437976416,0,0.0450136346124787,0,0,0,0,0,0,0,0.131193766498998,0,0.592705896731132,0.483457425382718,0.728283499988408,0.704586764625545,0.77771085536735,0.579433096725967,0.757209384015368,0.722887401491444,0,0,0,0,0,0,0,0.150190273830493,0,0,0,0,0,0.596320065562419,0.408605602194887,0.608174013507023,0.549484870631742,0.628058653281568,0,0,0,0,0.316264741738924,0.391312080128897,0.605825028266788,0.528218953826986,0,0,0,0.616910262804917,0.615017525836004,0,0,0.075701800770495,0.554448991642341,0,0.366485970110308,0,0,0.308262449175351,0,0,0.034807832411276,0,0,0,0,0,0,0,0.209868392808341,0,0,0,0,0,0,0,0,0,0.0859671683977995,0,0,0,0,0,0,0.0745624554111287,0.179335778193877,0,0.0952210875623146,0,0.769250573015581,0.831919712260684,1.12926073129168,0,0,0.0633754845527451,0,0,0,0,0,0,0.807626856296985,0,0.684431318033019,0.776870632432989,0.248935903763919,0,0,0,0.288969969315705,0.0858366336134482,0.13990914075318,0.0210885961662291,0,0,0,0.0612855891386548,0.0931854656348295,0.705744374215109,0.879969198479301,0.0839445661171913,0.234059791889601,0,0.0261550693490902,0,0.063963868687734,0.113693204094088,0.0427731395788809,0.226462404668981,0.0283076897745917,0.11745050892461,0.0623597393457245,0,0,0,0,0,0.0725376162611522,0.258587567436989,0,0,0
|full_id=C808_Neural_spinal_cerebral_hippocampus_cerebellum_duodenum_corpus
|full_id=C808_Neural_spinal_cerebral_hippocampus_cerebellum_duodenum_corpus
|gostat_on_coexpression_clusters=GO:0007167!enzyme linked receptor protein signaling pathway!0.00777254054695249!5764;780$GO:0007185!transmembrane receptor protein tyrosine phosphatase signaling pathway!0.0176603039176693!5764$GO:0007612!learning!0.0294277743350421!5764$GO:0030282!bone mineralization!0.0294277743350421!5764$GO:0004864!protein phosphatase inhibitor activity!0.0343248214812073!5764$GO:0019212!phosphatase inhibitor activity!0.0343248214812073!5764$GO:0007611!learning and/or memory!0.0369818444756987!5764$GO:0008201!heparin binding!0.0373143987937461!5764$GO:0019888!protein phosphatase regulator activity!0.0373143987937461!5764$GO:0019208!phosphatase regulator activity!0.0373143987937461!5764$GO:0007166!cell surface receptor linked signal transduction!0.0373143987937461!5764;780$GO:0031214!biomineral formation!0.0373143987937461!5764$GO:0001503!ossification!0.0373143987937461!5764$GO:0046849!bone remodeling!0.0373143987937461!5764$GO:0048771!tissue remodeling!0.0373143987937461!5764$GO:0004714!transmembrane receptor protein tyrosine kinase activity!0.0373143987937461!780$GO:0005539!glycosaminoglycan binding!0.0373143987937461!5764$GO:0030247!polysaccharide binding!0.0373143987937461!5764$GO:0001871!pattern binding!0.0373143987937461!5764$GO:0019199!transmembrane receptor protein kinase activity!0.0373143987937461!780
|gostat_on_coexpression_clusters=GO:0007167!enzyme linked receptor protein signaling pathway!0.00777254054695249!5764;780$GO:0007185!transmembrane receptor protein tyrosine phosphatase signaling pathway!0.0176603039176693!5764$GO:0007612!learning!0.0294277743350421!5764$GO:0030282!bone mineralization!0.0294277743350421!5764$GO:0004864!protein phosphatase inhibitor activity!0.0343248214812073!5764$GO:0019212!phosphatase inhibitor activity!0.0343248214812073!5764$GO:0007611!learning and/or memory!0.0369818444756987!5764$GO:0008201!heparin binding!0.0373143987937461!5764$GO:0019888!protein phosphatase regulator activity!0.0373143987937461!5764$GO:0019208!phosphatase regulator activity!0.0373143987937461!5764$GO:0007166!cell surface receptor linked signal transduction!0.0373143987937461!5764;780$GO:0031214!biomineral formation!0.0373143987937461!5764$GO:0001503!ossification!0.0373143987937461!5764$GO:0046849!bone remodeling!0.0373143987937461!5764$GO:0048771!tissue remodeling!0.0373143987937461!5764$GO:0004714!transmembrane receptor protein tyrosine kinase activity!0.0373143987937461!780$GO:0005539!glycosaminoglycan binding!0.0373143987937461!5764$GO:0030247!polysaccharide binding!0.0373143987937461!5764$GO:0001871!pattern binding!0.0373143987937461!5764$GO:0019199!transmembrane receptor protein kinase activity!0.0373143987937461!780

Revision as of 18:32, 12 September 2012


Full id: C808_Neural_spinal_cerebral_hippocampus_cerebellum_duodenum_corpus



Phase1 CAGE Peaks

Hg19::chr11:82444874..82444886,-p2@FAM181B
Hg19::chr11:82444929..82444940,-p4@FAM181B
Hg19::chr3:147657764..147657816,+p1@ENST00000467198
p1@ENST00000485006
p1@uc003ewf.1
Hg19::chr6:30848740..30848768,+p8@DDR1
Hg19::chr6:30848771..30848818,+p7@DDR1
Hg19::chr7:136936091..136936115,-p@chr7:136936091..136936115
-
Hg19::chr7:137028434..137028487,-p2@PTN
Hg19::chr7:137028498..137028519,-p6@PTN
Hg19::chr7:137028534..137028548,-p3@PTN
Hg19::chrX:70389721..70389757,+p@chrX:70389721..70389757
+


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:0007167enzyme linked receptor protein signaling pathway0.00777254054695249
GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway0.0176603039176693
GO:0007612learning0.0294277743350421
GO:0030282bone mineralization0.0294277743350421
GO:0004864protein phosphatase inhibitor activity0.0343248214812073
GO:0019212phosphatase inhibitor activity0.0343248214812073
GO:0007611learning and/or memory0.0369818444756987
GO:0008201heparin binding0.0373143987937461
GO:0019888protein phosphatase regulator activity0.0373143987937461
GO:0019208phosphatase regulator activity0.0373143987937461
GO:0007166cell surface receptor linked signal transduction0.0373143987937461
GO:0031214biomineral formation0.0373143987937461
GO:0001503ossification0.0373143987937461
GO:0046849bone remodeling0.0373143987937461
GO:0048771tissue remodeling0.0373143987937461
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0373143987937461
GO:0005539glycosaminoglycan binding0.0373143987937461
GO:0030247polysaccharide binding0.0373143987937461
GO:0001871pattern binding0.0373143987937461
GO:0019199transmembrane receptor protein kinase activity0.0373143987937461



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
non-terminally differentiated cell6.78e-08180
Uber Anatomy
Ontology termp-valuen
central nervous system2.57e-4482
regional part of nervous system7.62e-4494
nervous system7.62e-4494
ectoderm-derived structure1.14e-37169
ectoderm1.30e-37173
presumptive ectoderm1.30e-37173
neural tube8.33e-3757
neural rod8.33e-3757
future spinal cord8.33e-3757
neural keel8.33e-3757
brain4.04e-3669
future brain4.04e-3669
regional part of brain1.63e-3559
neural plate3.78e-3586
presumptive neural plate3.78e-3586
adult organism5.17e-35115
head6.04e-35123
anterior region of body1.41e-34129
craniocervical region1.41e-34129
neurectoderm1.51e-3490
anterior neural tube1.99e-2742
regional part of forebrain4.28e-2741
forebrain4.28e-2741
future forebrain4.28e-2741
pre-chordal neural plate4.84e-2561
organism subdivision2.64e-23365
telencephalon8.70e-2334
gray matter8.81e-2334
brain grey matter8.81e-2334
regional part of telencephalon3.45e-2233
cerebral hemisphere2.31e-2132
multi-tissue structure3.83e-20347
cerebral cortex5.30e-1725
pallium5.30e-1725
regional part of cerebral cortex2.81e-1522
multi-cellular organism3.02e-15659
neocortex5.01e-1420
organ9.21e-14511
cell layer3.18e-13312
organ part8.24e-13219
epithelium1.73e-12309
embryo3.13e-12612
anatomical cluster5.01e-12286
anatomical system1.36e-11625
anatomical conduit1.53e-11241
anatomical group2.30e-11626
posterior neural tube2.39e-1015
chordal neural plate2.39e-1015
tube2.76e-10194
embryonic structure5.40e-10605
developing anatomical structure5.40e-10605
germ layer1.08e-09604
embryonic tissue1.08e-09604
presumptive structure1.08e-09604
epiblast (generic)1.08e-09604
segmental subdivision of nervous system5.46e-0913
segmental subdivision of hindbrain2.44e-0812
hindbrain2.44e-0812
presumptive hindbrain2.44e-0812
basal ganglion3.12e-079
nuclear complex of neuraxis3.12e-079
aggregate regional part of brain3.12e-079
collection of basal ganglia3.12e-079
cerebral subcortex3.12e-079
nucleus of brain3.14e-079
neural nucleus3.14e-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


This analysis result is provided for C0 - C305 clusters.