Personal tools

Coexpression cluster:C1120: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:38, 17 September 2013


Full id: C1120_adult_hairy_mycosis_B_plasma_CD4_cord



Phase1 CAGE Peaks

Hg19::chr10:69513561..69513563,-p@chr10:69513561..69513563
-
Hg19::chr5:95309942..95309984,+p@chr5:95309942..95309984
+
Hg19::chr7:142494920..142494955,+p1@TRBJ2-6
Hg19::chr8:102980193..102980205,-p@chr8:102980193..102980205
-
Hg19::chr8:102987548..102987571,-p4@NCALD
Hg19::chr8:102987581..102987599,-p5@NCALD
Hg19::chr8:103108677..103108680,-p@chr8:103108677..103108680
-


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:0030276clathrin binding0.00647592134699164
GO:0030130clathrin coat of trans-Golgi network vesicle0.00647592134699164
GO:0012510trans-Golgi network transport vesicle membrane0.00647592134699164
GO:0030125clathrin vesicle coat0.00647592134699164
GO:0030665clathrin coated vesicle membrane0.00647592134699164
GO:0030140trans-Golgi network transport vesicle0.00647592134699164
GO:0030658transport vesicle membrane0.00647592134699164
GO:0030660Golgi-associated vesicle membrane0.00647592134699164
GO:0030120vesicle coat0.0079792602311147
GO:0030662coated vesicle membrane0.0079792602311147
GO:0030133transport vesicle0.0079792602311147
GO:0030118clathrin coat0.0079792602311147
GO:0015631tubulin binding0.0079792602311147
GO:0005798Golgi-associated vesicle0.0079792602311147
GO:0030659cytoplasmic vesicle membrane0.00939008595313787
GO:0044433cytoplasmic vesicle part0.00939008595313787
GO:0012506vesicle membrane0.00939008595313787
GO:0030136clathrin-coated vesicle0.00939008595313787
GO:0030117membrane coat0.00939008595313787
GO:0048475coated membrane0.00939008595313787
GO:0030135coated vesicle0.0113328623572354
GO:0016023cytoplasmic membrane-bound vesicle0.0246219926213745
GO:0031988membrane-bound vesicle0.0246219926213745
GO:0000139Golgi membrane0.0246219926213745
GO:0044431Golgi apparatus part0.0253254781248423
GO:0031410cytoplasmic vesicle0.0253254781248423
GO:0031982vesicle0.0253254781248423
GO:0003779actin binding0.0253254781248423
GO:0005829cytosol0.031648454324814
GO:0008092cytoskeletal protein binding0.031648454324814
GO:0016192vesicle-mediated transport0.031648454324814
GO:0005794Golgi apparatus0.0351622291887437



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
hemopoietic organ6.77e-127
immune organ6.77e-127
vermiform appendix2.08e-101
caecum2.08e-101
midgut2.08e-101
tonsil2.50e-101
mucosa-associated lymphoid tissue2.50e-101
lymphoid tissue2.50e-101
tonsillar ring2.50e-101
thymus1.12e-094
hemolymphoid system gland1.12e-094
thymic region1.12e-094
pharyngeal gland1.12e-094
thymus primordium1.12e-094
umbilical cord8.05e-0910
blastocyst8.05e-0910
blastula8.05e-0910
bilaminar disc8.05e-0910
inner cell mass8.05e-0910
cleaving embryo8.05e-0910
connecting stalk8.05e-0910
inner cell mass derived epiblast8.05e-0910
extraembryonic mesoderm8.05e-0910
chordate pharynx1.69e-0810
pharyngeal region of foregut1.69e-0810
pharynx9.03e-0811
pharyngeal epithelium9.81e-076
Disease
Ontology termp-valuen
lymphoma1.45e-4310
non-Hodgkin lymphoma7.40e-111
cutaneous T cell lymphoma7.40e-111
mycosis fungoides7.40e-111
hematologic cancer1.97e-1051
immune system cancer1.97e-1051
anemia3.61e-101


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)
MA0003.10.0462779
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.11.04442
MA0060.11.19421
MA0061.12.43031
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.11.70839
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.11.26109
MA0092.11.17914
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.11.68581
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.11.83012
MA0143.10.66587
MA0144.11.30855
MA0145.10.0807715
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.611548
MA0137.20.95459
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.485816
MA0163.10.0765396
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.000432051
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
MA0442.10



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
POU2F2#545245.203499461567160.003866714310179810.0190605454212899



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:C1120&oldid=3068237"