Personal tools

Coexpression cluster:C3395: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0.153163150959913,0,0.160456854061196,0,0.474360313060817,0,0.251286965243594,0.23985027306034,0.958400927334568,0,0,0,0.220838645003429,0,0,0,0,0.0956024239401108,0,0,0.723746183285228,0.65884435227135,0.731910329065423,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0500199076189239,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0614539199911022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0522561809686404,0.318963865966379,0,0.271627684441639,0,0,0.121343715517125,0.0869750240711818,0,0.375714865498416,0,0.136969166919767,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.101430488564433,0,0.028244987099354,0,0,0,0,0,0,0,0,0,0,0,0.210671632826821,0,0,0,0,0.0570765567424092,0,0.0503156775564332,0,0,0.0959594073735869,0,0,0,0,0,0.0842708651870891,0,0,0,0,0,0,0.113973783953524,0,0,0,0,0.0375838715958513,0.103715102399308,0.0321184467178978,0,0.131942369721337,0.11469646534793,0.126819880545037,0,0,0,0.321756494657324,0.340992667876797,0.456229814272213,0.424649223681157,0.576977851819394,0.390919118470156,0,0,0,0,0.23600275090536,0.542133339716909,0.504008588531179,0.388468202870498,0.441648572334016,0.363099673708455,0.422514706559592,0.41796561077571,0.337924015273307,0.567406366261856,0,0,0,0,0,0,0,0,0.208156981259094,0,0.0452252653904662,0,0,0,0,0,0,0.713783998360351,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.159713114533486,0.140504405746413,0,0.433085374649978,0.0425075842205678,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0366592590783005,0.0757292634393809,0,0,0,0,0,0,0.288208658361925,0.751258534313624,0.56587853039173,0.828753238223693,0,0,0,0,0,0,0,0,0,0.0914146875965646,0,0,0,0,0.0625372569970482,0,0,0.48555967742772,0,0,0,0.344885298375197,0,0,0,0,0.107433877051114,0.0990858576492829,0,0,0,0,0,0,0,0,0.430080265486803,0.227796366359549,0,0.015990885937406,0,0,0.161727153872444,0.164974707547417,0.251479989016808,0,0.216243565934643,0,0,0,0,0.258359310587411,0.545115151677475,0.0986009078228607,0.188923197856126,0.409446725650392,0,0,0.484527748672798,0,0,0.0425916600387234,0.407676527327578,0.380692589104479,0,0,0,0.0400762477245316,0.0428568528008729,0.0620189823948138,0.0765156238673234,0,0,0.247246293801826,0.575187048533518,0.124037672048917,0,0,0.00623529365639677,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0718350632709503,0,0,0,0,0,0,0.0209371702093587,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00412883216831599,0,0,0.213072052700123,0.298391186510551,0,0.056529592902869,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.4328386845022,0,0.0951833797824107,0,0,0,0,0.14586699057442,0,0,0.217284881323851,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.318443742632955,0.221712516823753,0,0,0,0.163801560828555,0,0,0.498131334169749,0,0.330332424119025,0.299757310563537,0.381420904865587,0,0,0.265879043943754,0.254546132326747,0.0321641214287157,0.472676505836724,0.0422874684771159,0.0955771563476108,0,0,0,0,0.174122933842314,0,0,1.40197437210437,0.637454857850738,1.10152465973817,0,0.15754742557206,0.236788992518656,0.413820651241493,0.63400316231321,0.0183714948889723,0.227754789214255,0.111129587570977,0.108310342108112,0.563151579795656,0.707593926525251,0.402401944384513,0.22101642443278,1.30557910431975,0.473409384912369,0,0.151759294076614,0.208334400411299,0,0,0,0.0487413906690946,0.120245177400006,0,0.315144937492197,0,0.409899758085875,0.175695884392047,0.161724672450793,0.251455738841334,0.177093253311778,0.195695236438374,0.169324547093176,0,0,0.298737722087551,0.0112891808582404,1.03951799280053,0.070745145653078,0.851888013529775,0,0,0,0.460481640888346,0.255893981334376,0.736478131510894,0,0.0696467370250307,0,0.144444803709627,0.46021935203868,0.2828980264685,0,0.37160545850754,0.457334892941399,0,0,0,0,0.195683583376492,0,0.378121228432484,0,0.0362531985397609,0.1301578714358,0.46117521531749,0.293928716124739,0.306049643341116,0.332360966533257,0.390022350398684,0,0.915472846746208,0,0,0.515766402705693,0.0775682460801064,0,0.315396146312343,0.342197116324734,0.156025274855562,0.208678686283756,0.0687775087883389,0,0.0508638757203747,0.0919109500998384,0,0,0,0,0.447353554180645,0.260413027427314,0,0,0,0.106966425460878,0.163853084473343,0.161207885486259,0.414544187344666,0.602557227482913,0.0874873383132558,0.223193341508521,0,0,0.190746818647884,0.28025376696736,0.187303053977226,0.201723357455821,0,0.529647071424384,0.397633717386723,0.388594626592444,0.400181048259343,0.351471819906173,0,0,0.618986513017405,0,0.212306328653727,0.252080518603097,0,0.23480807165701,0.076245357210966,0.497494413877184,0.750866466288746,0,0,0,0,0,0.145471226792492,0,0,0,0.696811125811939,0.504852691341208,0.365923187681077,0,0,0.0469099204222127,0,0,0,0,0,0,0,0,0,0.0493732449734086,0,0.734827094095294,0.487766940539148,0.477563270518182,0.587379335783582,0.300674046226905,0.43754434799617,0.056275291093238,0.327322895984986,0.0613201791501264,0,0,0.450180973779441,0.304155888786008,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.255285902718873,0.153278206181897,0,0,0,0,0,0,0,0,0,0,0,0.0576360315331177,0,0.0526355714321349,0,0,0.115230947587976,0.424734871537222,0,0,0,0,0.0954388822399226,0,0.0791766844314576,0,0,0,0,0,0.210071535945973,0.0989165855502945,0.244221111706559,0.0449879496849636,0.189223026931497,0.126931389473126,0,0.299177282574157,0,0.046133669228188,0,0.181627015791724,0.131193766498998,0.209232147197956,0.582754716689817,0,0.357376547979255,0.260182442680742,0.400094001166251,0.805790677957396,0.688011633279246,0.586068136921517,0,0.0919971935600616,0.116628593232515,0,0,0,0.129453387482482,0.0883597317803446,0.00601471838613701,0,0,0.123048870237934,0.0598874413026267,0.654364701821813,0.754842644731321,0.350271434513732,0.620218376667176,0.421755973572414,0,0.29938140626407,0,0,0.497317759250607,0.125898678133584,0,0.0890788809625826,0,0,0,0.360105633121321,0.818930604758036,0.679627999232671,0.176299951293199,0.21163965958111,0.780151548355891,0,0.451220938524739,0,0,0.487537089915036,0.484894195549175,0.490288032586266,0,0,0.150582174035777,0.268014236710241,0,0.155405081403798,0,0,0,0,0.117339711759041,0,0,0,0,0,0.081104385612865,0.334416438693572,0.098151162183357,0.580614083013793,0.20326475509102,0.01888140161532,0.0464741249455258,0.123793366570605,0.0884491207876909,0.11683898487757,0.218976056853198,0,0.692174532975451,0,0.596005943773614,0.202513600396907,0.355636766070246,0,0,0,0,0.0588311967140124,0,0,0.238130540907848,0.0901915267174634,0.434580878552298,0.168295518090842,0.906933534245014,0,0.313456698449451,0,0.164999540860188,0,0.303051570769615,0.189301580535783,0.21311714614554,0.178960883481455,0.102851129332916,0,0.0971557677904766,0.139530721565415,0.103106967823645,0.424610342996058,0.261848822492894,0.0101613915049496,0.234059791889601,0,0,0.278079899524469,0.160027141720365,0.382884822143586,0.0855462791577618,0.306789446764709,0.0283076897745917,0.084635829807314,0.124719478691449,0,0.0440406409639688,0,0,0.524579074618365,0.20715139958257,0.14826204992358,0,0.0796420028184954,0
|full_id=C3395_brain_colon_cerebellum_eye_temporal_rectum_diencephalon
|full_id=C3395_brain_colon_cerebellum_eye_temporal_rectum_diencephalon
|id=C3395
|id=C3395

Revision as of 16:18, 12 September 2012


Full id: C3395_brain_colon_cerebellum_eye_temporal_rectum_diencephalon



Phase1 CAGE Peaks

Hg19::chr14:103988232..103988265,+p@chr14:103988232..103988265
+
Hg19::chr14:103988347..103988399,+p@chr14:103988347..103988399
+
Hg19::chr14:103988435..103988448,+p@chr14:103988435..103988448
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube5.17e-3157
neural rod5.17e-3157
future spinal cord5.17e-3157
neural keel5.17e-3157
regional part of nervous system8.13e-3194
nervous system8.13e-3194
central nervous system3.07e-3082
adult organism1.96e-27115
neurectoderm1.04e-2590
neural plate1.45e-2586
presumptive neural plate1.45e-2586
anterior neural tube8.14e-2542
brain9.15e-2569
future brain9.15e-2569
regional part of forebrain1.93e-2441
forebrain1.93e-2441
future forebrain1.93e-2441
regional part of brain2.55e-2459
telencephalon5.02e-2234
gray matter6.19e-2234
brain grey matter6.19e-2234
regional part of telencephalon2.41e-2133
cerebral hemisphere6.97e-2132
ectoderm8.22e-20173
presumptive ectoderm8.22e-20173
organ part1.05e-19219
pre-chordal neural plate1.34e-1961
ectoderm-derived structure2.10e-19169
cerebral cortex2.02e-1625
pallium2.02e-1625
head4.77e-16123
anterior region of body3.61e-15129
craniocervical region3.61e-15129
regional part of cerebral cortex2.22e-1422
organ1.65e-13511
neocortex2.89e-1320
multi-tissue structure5.10e-13347
organism subdivision1.98e-12365
multi-cellular organism3.31e-11659
embryo2.17e-10612
anatomical system1.31e-09625
anatomical group2.00e-09626
epithelium2.21e-08309
embryonic structure2.67e-08605
developing anatomical structure2.67e-08605
germ layer4.31e-08604
embryonic tissue4.31e-08604
presumptive structure4.31e-08604
epiblast (generic)4.31e-08604
cell layer7.90e-08312
anatomical cluster1.74e-07286
posterior neural tube2.02e-0715
chordal neural plate2.02e-0715
nucleus of brain5.72e-079
neural nucleus5.72e-079
basal ganglion7.62e-079
nuclear complex of neuraxis7.62e-079
aggregate regional part of brain7.62e-079
collection of basal ganglia7.62e-079
cerebral subcortex7.62e-079
tube8.06e-07194
segmental subdivision of nervous system9.03e-0713


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

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

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0189565756827322
E2F1#186934.907389214879320.008460985347239390.0324265842971023
ZBTB7A#5134137.35190930787590.002516255860282270.0139821891881894



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3395&oldid=2138179"