Personal tools

Coexpression cluster:C1466: 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 11:45, 17 September 2013


Full id: C1466_immature_Mast_CD14_Eosinophils_CD8_CD4_Basophils



Phase1 CAGE Peaks

Hg19::chr1:16163919..16163931,+p@chr1:16163919..16163931
+
Hg19::chr9:102584241..102584261,+p4@NR4A3
Hg19::chr9:102584262..102584276,+p1@NR4A3
Hg19::chr9:102584278..102584285,+p5@NR4A3
Hg19::chr9:102588066..102588078,+p2@S81242
Hg19::chr9:102628236..102628245,+p@chr9:102628236..102628245
+


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:0004887thyroid hormone receptor activity0.0123631225715295



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
myeloid leukocyte9.03e-3172
defensive cell1.25e-2748
phagocyte1.25e-2748
classical monocyte1.55e-2742
CD14-positive, CD16-negative classical monocyte1.55e-2742
granulocyte monocyte progenitor cell4.74e-2767
leukocyte1.11e-25136
macrophage dendritic cell progenitor1.40e-2461
myeloid lineage restricted progenitor cell2.37e-2366
monopoietic cell5.22e-2359
monocyte5.22e-2359
monoblast5.22e-2359
promonocyte5.22e-2359
myeloid cell9.20e-17108
common myeloid progenitor9.20e-17108
hematopoietic lineage restricted progenitor cell1.44e-16120
nongranular leukocyte1.07e-15115
hematopoietic stem cell4.68e-15168
angioblastic mesenchymal cell4.68e-15168
hematopoietic cell1.15e-13177
stuff accumulating cell5.54e-1387
hematopoietic oligopotent progenitor cell6.55e-13161
hematopoietic multipotent progenitor cell6.55e-13161
dendritic cell1.63e-0910
conventional dendritic cell3.30e-088
granulocyte1.37e-078
intermediate monocyte5.25e-079
CD14-positive, CD16-positive monocyte5.25e-079
Uber Anatomy
Ontology termp-valuen
bone marrow1.60e-2576
bone element3.82e-2482
skeletal system5.86e-22100
hematopoietic system1.91e-2198
blood island1.91e-2198
skeletal element1.11e-2090
immune system1.51e-1993
hemolymphoid system3.04e-17108
adult organism3.92e-09114
musculoskeletal system1.79e-07167


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)
MA0003.10.0799681
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.788761
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.11.41501
MA0042.10.544748
MA0043.12.36158
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.71708
MA0056.10
MA0057.11.41984
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.13.04208
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.13.14993
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.0213085
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.11.21643
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.22.83905
MA0099.20.629739
MA0079.21.95397
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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
BRCA1#672310.09211532161190.002171044253359580.0125271652362774
CTCFL#14069039.873237179487180.002312760027857710.0131194581798616
FOXA1#316935.540709874692730.01192178777860280.0433802380952372
JUN#372536.256414596168170.008486346850954870.032417907050727
RFX5#599336.023955413597550.009437904036335060.0356048713932523
STAT1#6772310.35329374859960.002016680459920930.011722607589118
SUZ12#23512325.05789045553150.0001517575983051030.00195502797698121
TCF7L2#693435.385088281568670.01290488779931040.0464109358427058



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:C1466&oldid=3068583"