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{{Coexpression_clusters
 
{{Coexpression_clusters
 +
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0.229886828011239,0,0.101667003219354,0,0,0,0,0,0,0.539379893408307,0.4202867974138,0.287883245271605,0.517181099614796,0.189630012295427,0.138816573042107,0.574133472052094,0.472817004579933,0.54638779533177,0.144064671875115,0,0.0625128387853364,0,0.114346030083907,0,0,0,0,0,0.0793782434714987,0.15655573578941,0,0,0,0.0589565109853561,0.139210117864267,0,0.165795549095301,0.348986669269068,0.28535904381024,0.197386646657653,0.0990452042849908,0.092187879276543,0.227755975528437,0.360019282223445,0.371855321441455,0.138771381856642,0.104796384789156,0.0880380456512581,0.207410238582937,0.466211111825445,0.46508698088545,0,0,0,0.334621998523167,0.329351182440039,0.351341005362286,0.097343627213097,0,0.362319030942428,0.205583124092593,0.393243529040083,0,0,0.0837191039350518,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.195681888795628,0,0.246633096772289,0,0,0.101535401656103,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.288997341132196,0.221463322705341,0.183841515445592,0.182961114915842,0,0.240940657106499,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.560577092055277,0.688224224545008,0.00358688342124575,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0503156775564332,0,0,0,0,0,0,0.135427931031567,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.178710225414154,0.158079164695268,0.926362826800478,0.808462190008375,0.943741477731467,0.6936495857979,0.848540132744215,0.503772188315232,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.356906685747724,0.12571701528169,0,0,0,0,0,0.414781163730515,0,0.298362323348138,0,0.133213135365203,0.0737831746122416,0,0,0,0.310347787595302,0,0,0,0,0,0,0,0,0,0,0.119698443341419,0.195096818407981,0,0,0,0.472851918038659,0.331352304330334,0.231651318992539,0.302945276961852,0.177527765965176,0,0.140504405746413,0,0,0,0,0.109182349273979,0.125934274376603,0.247937465857602,0.0575109031693576,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.088793487769067,0,0.146094520726236,0,0,0,0,0,0,0,0,0,0,0.144281939746476,0,0.052441152940763,0.246075866847322,0.361991832974167,0,0.176828584828355,0.214297657915009,0.242791553592671,0,0.262173581098575,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0776589694549609,0.172032804693735,0,0,0.121428558500853,0,0,0.0896748239484563,0,0,0,0,0,0,0,0,0,0,0,0,0.367254128645786,0.255761024149889,0.0938639559954845,0,0,0,0.371732441100379,0.228692365630881,0.52543993989795,0,0.119471955332098,0,0,0.0849035433286077,0,0.188054201617406,0.301763235794132,0.305244952580507,0.262706372468367,0.160693426449034,0,0,0.099145253918139,0.29755128547361,0.217683092140345,0.0425916600387234,0.261054639134477,0.333474076770968,0.430469802339611,0,0,0.171244687451929,0,0,0,0.0571553686541154,0,0.0355204411879812,0.102809556581045,0.066432124538699,0.0763454992192642,0.174913108959819,0.28112886235651,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.105352457754613,0.117825963998405,0,0,0,0.172496019467973,0,0,0,0,0,0,0,0,0.198320387665648,0,0,0,0,0,0,0,0,0,0,0,0.130312767515111,0.0398985583070718,0,0,0.19447626789484,0.15548949326123,0,0.159395773552723,0,0,0,0,0,0,0,0,0,0.264035290066757,0,0.392789276207984,0,0,0.233356205412612,0.169756354072204,0,0,0,0.196235471445381,0,0.281701056973614,0,0,0,0,0.0798320938648321,0.26756886175468,0.227117834445179,0.116355582210209,0.160574230329875,0.222038902954069,0,0,0,0,0,0,0.408614434258682,0,0,0,0.191409364113299,0,0,0,0.299757310563537,0.327431548746431,0.159938416493743,0,0.034377883739342,0.0789089986057754,0.376835919641402,0.302705522830785,0.080820276450175,0.371794071542173,0,0.10078017905008,0.112942256193696,0,0.0170587850746231,0,0,0.328480217627131,0.395202216134025,0,0,0,0,0.226022358086975,0.516969167765541,0,0.253366729894761,0.030883943172502,0.408685050915787,0,0.304741869741253,0.576262827415321,0.22101642443278,0.27568969562093,0.364797128903212,0,0.192482419495004,0.22854210410682,0,0.389359781352817,0.717554782822273,0.470653400737023,0,0.0380625695285996,0,0,0.050197747123139,0,0,0,0,0,0,0.212984640524252,0.330947111885972,0.452949634040394,0.217264351326445,0,0.2093012868032,0.492186002567039,0,0,0,0.345024663353883,0,0.166882495138135,0,0.337257085318794,0.0715753130339987,0,0.534002526650922,0.669583990839343,0.0300471133262784,0.447759582825635,0.33052945589219,0.116544217527645,0.220626815433903,0,0,0,0,0.182037609946382,0,0.477463018736572,0.177635109332951,0,0,0,0,0.0769963366386578,0.20892292156567,0.224777002410304,0,0.018877979634509,0.229533065350686,0,0.726611188307205,0.358071584125933,0,0.499873439802377,0.126254769289342,0.226955440748216,0,0.137593858891759,0.0919109500998384,0.225185446293564,0.332565964082565,0,0.198079800894878,0.204234048342335,0.105104912336182,0.357451879411068,0,0,0,0,0,0.203858513377274,0,0,0,0,0.752803999223227,0,0,0,0.144172393115712,0.0679432810511184,0.254120022070344,0.320068822863804,0.700602373832031,0.633564038157672,0.745843009675886,0.371038911293733,0.248905129112398,0.320871309748802,0,0.289068845040772,0.300299152802392,0.04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|full_id=C3203_testicular_Mast_H9_Eosinophils_iPS_immature_gall
 
|full_id=C3203_testicular_Mast_H9_Eosinophils_iPS_immature_gall
 
|id=C3203
 
|id=C3203

Revision as of 07:05, 12 September 2012


Full id: C3203_testicular_Mast_H9_Eosinophils_iPS_immature_gall



Phase1 CAGE Peaks

  Short description
Hg19::chr11:77184963..77185028,- p2@PAK1
Hg19::chr11:77185029..77185043,- p9@PAK1
Hg19::chr11:77185057..77185070,- p13@PAK1


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


No GOStat results

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
disease_data


Cell Type
Ontology termp-valuen
neural cell4.80e-0825
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.28e-2194
nervous system2.28e-2194
central nervous system4.33e-2182
neurectoderm6.28e-1790
neural plate7.67e-1786
presumptive neural plate7.67e-1786
brain1.22e-1669
future brain1.22e-1669
neural tube1.46e-1657
neural rod1.46e-1657
future spinal cord1.46e-1657
neural keel1.46e-1657
ectoderm2.19e-15173
presumptive ectoderm2.19e-15173
ectoderm-derived structure3.97e-15169
organ1.29e-14511
head1.70e-14123
regional part of brain2.98e-1459
anterior region of body3.11e-14129
craniocervical region3.11e-14129
pre-chordal neural plate5.19e-1461
telencephalon9.66e-1334
cerebral hemisphere1.39e-1232
regional part of forebrain1.51e-1241
forebrain1.51e-1241
future forebrain1.51e-1241
anterior neural tube2.30e-1242
gray matter2.47e-1234
brain grey matter2.47e-1234
regional part of telencephalon2.68e-1233
embryo6.49e-12612
cerebral cortex1.71e-1125
pallium1.71e-1125
adult organism1.47e-10115
regional part of cerebral cortex1.97e-1022
neocortex4.60e-1020
embryonic structure1.20e-09605
developing anatomical structure1.20e-09605
germ layer1.29e-09604
embryonic tissue1.29e-09604
presumptive structure1.29e-09604
epiblast (generic)1.29e-09604
organ part3.50e-09219
Disease
Ontology termp-valuen
cell type cancer1.99e-08143
carcinoma8.63e-08106


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
ATF3#467322.46317452600878.81932387510763e-050.00129292724058445
CCNT2#90536.336201576962630.003930750035764890.0189286058182059
CEBPB#105137.971147625824820.001974187055288560.0114973580475816
CTCF#1066435.360256373075030.0064925092527670.0278480091112462
CTCFL#140690319.74647435897440.0001298372005551160.00171234592609873
E2F6#187635.017155731697390.00791769806886330.0320684273874976
EGR1#195834.988179094810140.008056488137383440.0319260696103278
ELF1#199734.258097958807540.01295179875054610.0460312022632643
FOSL2#2355211.28680040304110.0100534586973120.0376590930342729
HMGN3#932438.178547723350590.001827766942164210.0108380259849366
IRF4#3662321.91451268674419.49854535978121e-050.00136172763051502
JUN#3725312.51282919233630.0005103313992726250.00443157071660711
JUND#372736.994663941871030.002921845042734990.0156233142749437
MEF2A#4205212.4954872730960.008235029478029740.0324758616341029
MYC#460935.22228187160940.007020843755740150.0293358632128724
NFKB1#479035.488063424193840.006049381815655430.0268698757047267
RAD21#5885310.35503389545630.0009004912073565420.00662112089588214
SIN3A#2594235.408884726815140.006318961977991520.0275586115179127
SMC3#9126315.04493284493280.0002935825420371870.00308155448319816
USF1#739136.361499277207960.00388404057290560.0189615908658761
ZBTB7A#5134137.35190930787590.002516255860282270.0139688112364864
ZEB1#6935316.88843201754390.0002075486917327580.00242110776453451
ZNF263#1012738.221841637010680.001799043925565870.0108972479145212



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.