Personal tools

Coexpression cluster:C1134: 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: C1134_Eosinophils_Neutrophils_CD19_CD8_Natural_CD4_Basophils



Phase1 CAGE Peaks

Hg19::chr11:121323670..121323687,-p1@ENST00000501964
p1@uc001pxw.1
Hg19::chr11:65407331..65407354,+p5@SIPA1
Hg19::chr13:25861394..25861408,-p7@MTMR6
Hg19::chr1:235490214..235490232,+p7@GGPS1
Hg19::chr22:40440895..40440904,+p12@TNRC6B
Hg19::chr6:30034656..30034686,-p@chr6:30034656..30034686
-
Hg19::chr7:43688351..43688370,-p3@C7orf44


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:0004337geranyltranstransferase activity0.0141267875544012
GO:0004161dimethylallyltranstransferase activity0.0141267875544012
GO:0046582Rap GTPase activator activity0.0141267875544012
GO:0004311farnesyltranstransferase activity0.0141267875544012
GO:0046839phospholipid dephosphorylation0.0493942937796945
GO:0004659prenyltransferase activity0.0493942937796945



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
leukocyte4.59e-72136
hematopoietic stem cell6.24e-59168
angioblastic mesenchymal cell6.24e-59168
nongranular leukocyte1.07e-54115
hematopoietic cell3.05e-54177
hematopoietic lineage restricted progenitor cell4.44e-52120
hematopoietic oligopotent progenitor cell7.93e-52161
hematopoietic multipotent progenitor cell7.93e-52161
lymphocyte7.69e-4453
common lymphoid progenitor7.69e-4453
lymphoid lineage restricted progenitor cell4.56e-4352
nucleate cell1.28e-4155
mature alpha-beta T cell1.65e-2318
alpha-beta T cell1.65e-2318
immature T cell1.65e-2318
mature T cell1.65e-2318
immature alpha-beta T cell1.65e-2318
lymphocyte of B lineage1.06e-2124
pro-B cell1.06e-2124
myeloid leukocyte3.11e-2072
classical monocyte5.54e-2042
CD14-positive, CD16-negative classical monocyte5.54e-2042
T cell2.31e-1825
pro-T cell2.31e-1825
defensive cell3.00e-1648
phagocyte3.00e-1648
B cell1.76e-1514
myeloid cell3.48e-15108
common myeloid progenitor3.48e-15108
CD8-positive, alpha-beta T cell8.06e-1511
granulocyte monocyte progenitor cell3.44e-1467
macrophage dendritic cell progenitor1.20e-1361
mesenchymal cell3.20e-13354
myeloid lineage restricted progenitor cell1.89e-1266
connective tissue cell2.00e-12361
monopoietic cell3.13e-1259
monocyte3.13e-1259
monoblast3.13e-1259
promonocyte3.13e-1259
granulocyte4.76e-128
motile cell1.09e-09386
CD4-positive, alpha-beta T cell1.36e-096
blood cell3.76e-0811
multi fate stem cell7.39e-07427
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.93e-2298
blood island2.93e-2298
hemolymphoid system1.03e-20108
immune system3.57e-1593
bone marrow5.83e-1376
connective tissue2.37e-11371
bone element3.14e-1182
skeletal element2.54e-0990
skeletal system2.00e-07100
blood2.88e-0715
haemolymphatic fluid2.88e-0715
organism substance2.88e-0715


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)
MA0003.10.213534
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.11.29551
MA0042.11.22641
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.11.22064
MA0058.10.406232
MA0059.10.404929
MA0060.11.86058
MA0061.11.09187
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.12.88764
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.13.16596
MA0074.11.46532
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.11.11391
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.11.64331
MA0103.10.88373
MA0105.11.14871
MA0106.10.648997
MA0107.11.3795
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
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.980834
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
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
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.632664
MA0164.11.62495
MA0080.20.344472
MA0018.21.56673
MA0099.20.572
MA0079.20.0109305
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
CHD2#110657.38858773865490.0001498689600820670.00193165053955461
EBF1#187956.361762033263580.0003078439918611820.00316913934608083
ELF1#199763.649798250406460.0009377479782620690.00678895474155776
NFKB1#479075.488063424193846.66568321176054e-060.000194566039394371
PAX5#507943.811180303530190.01208261681555190.043824978037071
POU2F2#545245.203499461567160.003866714310179810.019061445097747
TBP#690863.177232017511190.002074112051852660.0120156527947326
ZEB1#693549.650532581453630.0003718916645689250.00369834255912341



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:C1134&oldid=3068251"