Personal tools

Coexpression cluster:C3199: 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=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0877514257027229,0,0.180455955570557,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.123803082231165,0,0.154187968871398,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.12206750241012,0.129773480880396,0.102404861888327,0.092892723212638,0.196451135708678,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0428357178336246,0,0,0,0,0,0,0,0.232955676008343,0.303521794477971,0.236293617851166,0.345027274427113,0.320021012625357,0.384465193328721,0.370755997408503,0.375398431596482,0.141370482160471,0,0,0,0,0,0,0,0,0.861678377162507,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0955936734149088,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.492528432668985,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.629736230742571,0.0793645050922885,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.116980464645417,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.19447626789484,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.126645485425697,0,0,0,0,0.116355582210209,0.0876664805795525,0.125057592200758,0.143257247232019,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.080820276450175,0,0,0,0.0715216048933879,0,0,0,0,0,0,0,0.182087959020526,0.425165631111842,0,0.04680465889238,0,0.424017702901881,0.128639412800133,0,0,0,0,0,0,0,0,0.72004348249105,0,0,0,0.601770085216892,0.40241270641937,0.245643825533731,0,0.0380625695285996,0,0,0.0633259478784096,0,0,0,0,0,0,0,0,0.763877362770661,0,0,0,0,0,0,0,0,0,0,0,0.200575245617706,0.171890419039995,0,0,0,0.0266094859650764,0,0,0,0,0,0,0,0,0,0.0405993330353711,0.0697118989465167,0,0,0.110680260976652,0,0,0.0402022792589852,0,0,0,0,0,0,0.0334876163089719,0,0,0,0,0.460528757535925,0,0,0,0,0.0432061579680018,0.0806252010881579,0,0,0,0,0,0,0.106966425460878,0,0,0.379804443673228,0,0,0,0,0,0,0.0343941464470872,0,0.0407713899614982,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.179913699935071,0.381950369584154,0,0,0,0,0.078316005475075,0,0,0,0,0,0,0.322090781168434,0,0,0,0,0.0456863240084368,0.0261639379934246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0562408777463757,0,0,0,0,0.596517365589807,0,0,0.0839980704288979,0,0,0,0,0,0,0,0,0.0450136346124787,0,0,0,0,0,0,0.623485295623849,0,0,0,0,0,0,0,0.0290415862703977,0,0,0,0,0,0,0,0,0,0,0,0,0.830071780344843,0,0,0,0,0,0,0,0,0,0,0.052217621604872,0,0,0,0,0.383678581628569,0,0,0.0285589446518912,0.0276646214758744,0.131805147259529,0.125056264354711,0,0,0,0,0,0,0,0,0.165827456884257,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.049961086838963,0,0,0,0,0,0,0,0,0,0,0.0322859259446875,0,0,0,0,0,0,0,0,0.0390109377342095,0.0526615420969484,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.102851129332916,0.0381808373167472,0,0,0,0,0,0.0839445661171913,0,0,0,0,0,0.079946807131842,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C3199_cervical_mucinous_Intestinal_pancreatic_colon_placenta_bronchogenic
|full_id=C3199_cervical_mucinous_Intestinal_pancreatic_colon_placenta_bronchogenic
|id=C3199
|id=C3199

Revision as of 16:04, 12 September 2012


Full id: C3199_cervical_mucinous_Intestinal_pancreatic_colon_placenta_bronchogenic



Phase1 CAGE Peaks

Hg19::chr11:72983233..72983242,+p6@P2RY6
Hg19::chr11:72983246..72983253,+p7@P2RY6
Hg19::chr11:72983280..72983298,+p2@P2RY6


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
bone marrow5.16e-1680
bone element1.10e-1386
immune system9.97e-13115
hematopoietic system2.87e-12102
blood island2.87e-12102
organ8.70e-12511
hemolymphoid system7.31e-11112
larynx3.21e-109
skeletal element2.82e-09101
skeletal system2.82e-09101
adult organism2.59e-08115
upper respiratory tract1.01e-0719
Disease
Ontology termp-valuen
carcinoma8.01e-11106
cell type cancer3.96e-08143


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
EP300#203336.77394172622320.003216880500103790.0166957105078935
FOSL2#2355316.93020060456170.0002060162053171620.00242435227798525
FOXA1#3169311.08141974938550.000734755275698670.00579804353900214
FOXA2#3170324.63046375266526.68983856509345e-050.00107060994468249
GATA2#2624312.7449317335540.0004829527704283790.00436022686642198
GATA3#2625327.2365163572064.94721007899563e-050.0008492466690339
JUND#372736.994663941871030.002921845042734990.0156225144329186
MAFF#23764356.31535648994525.59409009993116e-060.000168807043035744
MAFK#7975327.10073313782995.02195559325033e-050.000856167189362507
MAX#414936.452555509007120.003721913834265510.0185862560455606
MYC#460935.22228187160940.007020843755740150.0293335160621573
NR3C1#2908314.9730233311730.0002978331194675480.00308035186809975
REST#597839.650028716128020.001112636247114590.00765548567180978
SMARCC1#6599343.66335931963151.20046018043203e-050.000301020073911503
SPI1#668838.204323508522730.001810593189410520.0108832542220918
TFAP2A#7020316.5186343730450.0002218033880766340.00247462066524256
TFAP2C#7022310.80922860986020.0007916746575753130.0061322932257293



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.