Personal tools

Coexpression cluster:C3357: 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=0,0,0.107857131651075,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.055712496781182,0.0513619522818629,0,0.0342676336102362,0,0.144064671875115,0.247398438714038,0,0,0,0,0,0.057730457053664,0,0,0.146465690858417,0.15655573578941,0,0,0,0,0,0,0,0,0,0,0.0990452042849908,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0832356854652995,0,0.0826628337153937,0.0462331160303238,0,0,0.108907434678255,0,0.0728614336604499,0,0,0,0,0,0,0,0,0.195681888795628,0,0.331795568716987,0,0.326544175202668,0,0.376023406467856,0.251886688790383,0.387249279609498,0,0.122518063916678,0.383876991441342,0.469566853250347,0,0.112137584435249,0.0869055220883388,0,0,0,0,0,0,0.276397316759331,0.18613148201837,0.310768747319633,0,0.140891414760007,0,0.0979578962680575,0.214083386736107,0,0.462533370184438,0.204743961790246,0.0989803802232471,0,0.168366204242204,0,0.302771000606212,0.186074537919819,0.362373064555405,0,0,0,0,0,0.0587472679543123,0,0,0.10843121454309,0,0.0702852779578603,0.29717881608204,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0834782173702644,0,0.0425961947748989,0,0,0,0,0,0.07338830676488,0,0,0,0,0,0,0,0,0,0.0477396614475454,0.0818231540625959,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.158803529189909,0.050375285110278,0,0,0,0,0,0,0,0,0.284981597615683,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0366482282265911,0.081825314342242,0.0584715597507662,0.0516318862226721,0,0,0,0,0,0,0,0,0,0,0.0527984507438095,0,0,0.367298244179727,0.309645999537164,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0461380391803668,0.201695368707335,0.270098683018587,0.306798958192767,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.150306889650249,0,0.185722801069447,0,0,0,0,0.116250315550445,0.107433877051114,0.247687297406738,0.306084857468188,0.171012795094276,0,0,0,0,0,0,0.0495511575604446,0,0,0,0,0,0,0,0.251479989016808,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0813768443325499,0,0,0,0,0,0,0,0,0,0,0,0,0.0370406554214911,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0555694062070307,0.153575950653048,0,0,0,0,0,0,0,0,0,0,0,0,0,0.312925547126707,0,0,0,0,0,0,0.0749215657724743,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.325512360804129,0,0,0,0,0,0.0892813554627994,0,0,0,0,0,0,0,0,0,0,0.0775089264793031,0,0,0,0,0,0.535651920568964,0,0,0.0458873451077849,0.108611070985339,0.291141860941089,0.11292814946238,0,0.299757310563537,0.193869405101915,0,0.123723537352191,0.0831891152636857,0.0789089986057754,0.191050583413854,0.399949866955586,0,0,0.351053498032414,0.0373740412220293,0,0,0.228016161468994,0,0,0,0.378674284566139,0,0,0,0,0,0.30470904208241,0.461063332141631,0.648109485736051,0,0.0695293501927681,0.442712183231462,0.38866187964103,1.06746967086845,0.863502360126005,0.994159976009405,0.404097490429746,0,0,0.0902054036215435,0.0891573798126359,0,0,0,0.120245177400006,0.105439595179987,0,0,0,0,0,0,0,0,0,0,0.065666642656593,0,0,0.299999916441319,0.131564216321577,0.346755838223862,0,0,0.0431350293094685,0.103668463987428,0.255893981334376,0.336724278419932,0.07278454461533,0,0,0,0.344374029099016,0.2828980264685,0.195534142644022,0.060819961675157,0.38945575602958,0,0,0,0,0,0,0,0,0,0.0699368280688007,0,0,0,0,0.110915157511936,1.40109330171724,0.481990764418722,0,0,0.401307313074337,0,0,0.0840229578243582,0.079112335990984,0,0.797176337977218,0,0.109952815588116,0,0,0,0,0,0,0.531693604049223,0.105104912336182,0,0,0,0.192724864233909,0.282540931879661,0,0.203858513377274,0.155100922768919,0.0874873383132558,0.103370540733874,0.133634660878237,0.335449775449978,0,0,0,0,0,0.529647071424384,0.259407612295607,0.0647398703344467,0.055966461856338,0,0,0,0.333294403446253,0,0.338871785206897,0.401604379705614,0.0832161034844002,0,0,0.234186964128339,0.220655051407841,0,0,0,0,0,0,0,0,0,0,0.664634716396999,0.34046263952091,0,0,0.084066558699748,0,0.26208976562482,0,0,0,0,0.188652303681418,0,0,0,0.167660583822881,0.734827094095294,0.504671008893299,0.512342368404133,0.517675704141427,0.324136399811715,0.427583940827828,0,0,0,0,0,0.166825123124581,0.304155888786008,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.145536958608929,0,0,0,0.781568403237058,0,0.0843766322300271,0,0,0,0,0,0.54038098347827,0,0,0,0,0,0,0,0.424734871537222,0,0.145691822538464,0.0657907963604995,0,0,0,0,0.0839980704288979,0,0,0,0,0,0,0,0.0634331720967665,0,0,0.0837085814034122,0,0,0,0.252517463477207,0.255410190403965,0,0.537814540474206,0.446912632592005,0.720233523348293,0.32581050040079,0.61031359661283,0.244577704109922,0.487805230121737,0.417431244024471,0,0,0,0,0,0,0,0,0.0883597317803446,0,0.250789242335245,0,0,0.0598874413026267,0.568378150846791,0.408605602194887,0.456393542916647,0.44336355769989,0.320966228024776,0,0,0.0703597699327489,0.052217621604872,0,0,0.720056651329793,0.544599308732647,0,0,0,0.675625790820688,0.400153393753074,0,0,0.032817368032432,0.435887584584522,0,0.281751001695877,0.0849077133655763,0,0.132702316438765,0,0,0.378555268462101,0.255685217972019,0,0,0,0,0,0,0.153323010348428,0.227197610169401,0,0,0.192923317190906,0.595992732035785,0,0,0,0.334416438693572,0.171934336795599,0,0,0.0487990718960468,0.582478364980288,0,0.0610613035651264,0.0904423417827262,0.27282479499172,0,0.173272723322218,0.288407123604235,0.297003355453999,0,0.493217991705455,0,0.0748046823502985,0,0,0,0,0,0.238130540907848,0,0.0581752393062885,0.252575821636671,0.347104870127962,0.272468530679021,0.184415109078388,0,0.454647098925123,0.270737776093534,0,0,0,0,0,0.105743346346567,0,0.0889635065466152,0,0.424610342996058,0.117370405459493,0.0839445661171913,0.092743246865863,0,0,0,0.0267975841371139,0,0,0.127828009549688,0.0283076897745917,0.084635829807314,0.124719478691449,0,0,0,0.18722485217892,0,0.20715139958257,0.628916856909537,0.221611588102807,0.146917605400546,0
|full_id=C3357_extraskeletal_uterus_cerebellum_small_gastric_mesothelioma_mesodermal
|full_id=C3357_extraskeletal_uterus_cerebellum_small_gastric_mesothelioma_mesodermal
|id=C3357
|id=C3357

Revision as of 16:16, 12 September 2012


Full id: C3357_extraskeletal_uterus_cerebellum_small_gastric_mesothelioma_mesodermal



Phase1 CAGE Peaks

Hg19::chr13:22245205..22245220,+p1@FGF9
Hg19::chr13:22245257..22245270,+p3@FGF9
Hg19::chr13:22245274..22245305,+p2@FGF9


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
mature alpha-beta T cell5.24e-0918
alpha-beta T cell5.24e-0918
immature T cell5.24e-0918
mature T cell5.24e-0918
immature alpha-beta T cell5.24e-0918
T cell1.58e-0725
pro-T cell1.58e-0725
lymphoid lineage restricted progenitor cell2.19e-0752
lymphocyte5.22e-0753
common lymphoid progenitor5.22e-0753
Uber Anatomy
Ontology termp-valuen
adult organism1.36e-30115
neural tube1.08e-2557
neural rod1.08e-2557
future spinal cord1.08e-2557
neural keel1.08e-2557
regional part of brain5.11e-2159
anterior neural tube7.11e-2142
regional part of forebrain9.56e-2141
forebrain9.56e-2141
future forebrain9.56e-2141
gray matter5.36e-1934
brain grey matter5.36e-1934
neural plate1.29e-1886
presumptive neural plate1.29e-1886
telencephalon1.51e-1834
cerebral hemisphere1.68e-1832
brain5.43e-1869
future brain5.43e-1869
neurectoderm6.46e-1890
regional part of telencephalon7.68e-1833
central nervous system5.40e-1782
regional part of cerebral cortex1.27e-1522
neocortex1.95e-1420
cerebral cortex2.07e-1425
pallium2.07e-1425
regional part of nervous system2.86e-1394
nervous system2.86e-1394
pre-chordal neural plate5.01e-1361
organ part1.61e-07219
anterior region of body3.98e-07129
craniocervical region3.98e-07129


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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139036383469521
CCNT2#90536.336201576962630.003930750035764890.0189521999439199
CTCF#1066435.360256373075030.0064925092527670.0278720475932972
E2F1#186934.907389214879320.008460985347239390.0324170677090258
E2F6#187635.017155731697390.00791769806886330.0321095200020974
EBF1#187938.9064668465690.00141523283560980.00913281649272444
EGR1#195834.988179094810140.008056488137383440.0319600244836172
ELF1#199734.258097958807540.01295179875054610.0460782432793393
ESR1#2099330.76860329615453.43136389821584e-050.000674765984119307
FOSL1#8061339.7135797163731.59554825631833e-050.000370552511322282
GABPB1#255337.067683836182170.002832212825417420.0153786770964838
HMGN3#932438.178547723350590.001827766942164210.0108472639886742
MYC#460935.22228187160940.007020843755740150.0293640583479134
NANOG#79923329.24477848101273.99627955670032e-050.000735708515110568
NRF1#4899312.21027944771090.0005492172401020010.00470122935325079
PAX5#507936.669565531177830.003370290999677260.0172535572626486
SP1#666735.69838137814090.005403962701712170.0245812047301445
SUZ12#23512350.11578091106297.93834897779404e-060.000221677333928297
TCF12#6938310.63446490218640.0008313523990202070.00628351521213427
TCF7L2#6934310.77017656313730.0008003181298398380.00612340111079435
YY1#752834.911170749853860.008441455341808260.0328459131344999
ZEB1#6935316.88843201754390.0002075486917327580.00242273139777328
ZNF143#7702313.50087655222790.0004062804962997170.00388282656964185
ZNF263#1012738.221841637010680.001799043925565870.0109099029463578



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.