Personal tools

Coexpression cluster:C1117: Difference between revisions

From FANTOM5_SSTAR

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

Latest revision as of 11:38, 17 September 2013


Full id: C1117_CD19_Eosinophils_Dendritic_Neutrophils_Basophils_CD14_CD34



Phase1 CAGE Peaks

Hg19::chr10:43932296..43932360,+p1@ZNF487P
Hg19::chr22:50629895..50629908,-p@chr22:50629895..50629908
-
Hg19::chr22:50630977..50630984,-p@chr22:50630977..50630984
-
Hg19::chr22:50639164..50639182,-p@chr22:50639164..50639182
-
Hg19::chr2:64880894..64880977,-p2@SERTAD2
Hg19::chr3:135914798..135914850,+p@chr3:135914798..135914850
+
Hg19::chr5:40681669..40681698,+p4@PTGER4


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:0004957prostaglandin E receptor activity0.0254229767174927
GO:0030278regulation of ossification0.0254229767174927
GO:0004955prostaglandin receptor activity0.0254229767174927
GO:0046850regulation of bone remodeling0.0254229767174927
GO:0004953icosanoid receptor activity0.0254229767174927
GO:0004954prostanoid receptor activity0.0254229767174927
GO:0030308negative regulation of cell growth0.0344450048876544
GO:0045792negative regulation of cell size0.0344450048876544
GO:0048856anatomical structure development0.0344450048876544
GO:0045926negative regulation of growth0.0344450048876544
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0354795642737389
GO:0019933cAMP-mediated signaling0.0354795642737389
GO:0031214biomineral formation0.0354795642737389
GO:0001503ossification0.0354795642737389
GO:0046849bone remodeling0.0361203882202558
GO:0048771tissue remodeling0.0370325943749413
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0382378355329935
GO:0019935cyclic-nucleotide-mediated signaling0.0382378355329935
GO:0001558regulation of cell growth0.0465793516965004
GO:0032502developmental process0.0465793516965004
GO:0003713transcription coactivator activity0.0471036744921992
GO:0016049cell growth0.0471036744921992
GO:0040008regulation of growth0.0471036744921992
GO:0008361regulation of cell size0.0471036744921992
GO:0001501skeletal development0.0471036744921992
GO:0045893positive regulation of transcription, DNA-dependent0.0483159197004316



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
leukocyte8.22e-85136
hematopoietic stem cell1.24e-75168
angioblastic mesenchymal cell1.24e-75168
hematopoietic cell2.98e-72177
hematopoietic oligopotent progenitor cell2.88e-69161
hematopoietic multipotent progenitor cell2.88e-69161
hematopoietic lineage restricted progenitor cell1.62e-66120
nongranular leukocyte1.17e-65115
myeloid leukocyte1.88e-4372
classical monocyte4.57e-3842
CD14-positive, CD16-negative classical monocyte4.57e-3842
granulocyte monocyte progenitor cell1.84e-3767
myeloid cell2.21e-37108
common myeloid progenitor2.21e-37108
defensive cell1.20e-3648
phagocyte1.20e-3648
macrophage dendritic cell progenitor1.28e-3361
myeloid lineage restricted progenitor cell7.40e-3366
monopoietic cell9.54e-3259
monocyte9.54e-3259
monoblast9.54e-3259
promonocyte9.54e-3259
lymphoid lineage restricted progenitor cell2.95e-2952
lymphocyte2.10e-2853
common lymphoid progenitor2.10e-2853
nucleate cell8.54e-2755
mesenchymal cell1.94e-18354
connective tissue cell2.30e-17361
stuff accumulating cell9.74e-1587
B cell2.17e-1414
T cell4.54e-1425
pro-T cell4.54e-1425
motile cell1.17e-13386
mature alpha-beta T cell1.80e-1318
alpha-beta T cell1.80e-1318
immature T cell1.80e-1318
mature T cell1.80e-1318
immature alpha-beta T cell1.80e-1318
lymphocyte of B lineage4.12e-1324
pro-B cell4.12e-1324
intermediate monocyte1.13e-119
CD14-positive, CD16-positive monocyte1.13e-119
granulocyte6.00e-118
stem cell3.91e-10441
multi fate stem cell4.85e-10427
somatic stem cell1.88e-09433
blood cell6.85e-0911
CD8-positive, alpha-beta T cell1.57e-0811
dendritic cell1.75e-0810
CD4-positive, alpha-beta T cell7.42e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.55e-4298
blood island3.55e-4298
hemolymphoid system4.48e-38108
bone marrow2.68e-3276
immune system3.17e-2993
bone element1.75e-2882
skeletal element3.17e-2490
skeletal system7.93e-21100
connective tissue6.49e-16371
lateral plate mesoderm5.78e-13203
blood6.47e-1015
haemolymphatic fluid6.47e-1015
organism substance6.47e-1015


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)
MA0003.12.47829
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.11.67472
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
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.649431
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.638423
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.11.70839
MA0074.10.60198
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.11.39213
MA0117.11.01134
MA0119.11.78583
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.04496
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.980834
MA0146.15.30418
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.21.14159
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.21.41281
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.534073
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.13878
MA0163.10.632664
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.22.09249
MA0102.21.51913
MA0258.11.27333
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
ELF1#199753.041498542005380.009719562269370750.036557833538042
PBX3#509039.391934008604630.002893813688341480.015644839413847



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:C1117&oldid=3068234"