Personal tools

Coexpression cluster:C1389: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:43, 17 September 2013


Full id: C1389_immature_CD19_CD14_Basophils_migratory_Natural_CD4



Phase1 CAGE Peaks

Hg19::chr14:105281710..105281738,+p1@AY927492
Hg19::chr6:32636347..32636362,+p@chr6:32636347..32636362
+
Hg19::chr6:32636372..32636386,+p@chr6:32636372..32636386
+
Hg19::chr6:32636402..32636417,+p@chr6:32636402..32636417
+
Hg19::chr7:128786662..128786710,+p@chr7:128786662..128786710
+
Hg19::chr7:129133189..129133195,+p@chr7:129133189..129133195
+


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><br>

Cell Type
Ontology termp-valuen
leukocyte1.87e-90136
nongranular leukocyte2.15e-77115
hematopoietic lineage restricted progenitor cell1.65e-73120
hematopoietic stem cell1.68e-69168
angioblastic mesenchymal cell1.68e-69168
hematopoietic cell7.52e-67177
hematopoietic oligopotent progenitor cell2.28e-62161
hematopoietic multipotent progenitor cell2.28e-62161
classical monocyte8.89e-6142
CD14-positive, CD16-negative classical monocyte8.89e-6142
defensive cell1.08e-5448
phagocyte1.08e-5448
macrophage dendritic cell progenitor1.17e-5061
granulocyte monocyte progenitor cell1.72e-4767
monopoietic cell1.21e-4659
monocyte1.21e-4659
monoblast1.21e-4659
promonocyte1.21e-4659
myeloid leukocyte1.28e-4572
myeloid lineage restricted progenitor cell7.96e-4366
myeloid cell2.82e-35108
common myeloid progenitor2.82e-35108
stuff accumulating cell3.74e-2587
lymphoid lineage restricted progenitor cell1.61e-2452
lymphocyte6.64e-2453
common lymphoid progenitor6.64e-2453
mesenchymal cell1.90e-23354
nucleate cell9.63e-2355
connective tissue cell1.33e-22361
motile cell1.24e-19386
lymphocyte of B lineage2.70e-1924
pro-B cell2.70e-1924
intermediate monocyte2.20e-169
CD14-positive, CD16-positive monocyte2.20e-169
stem cell2.32e-16441
dendritic cell2.58e-1610
multi fate stem cell5.18e-16427
somatic stem cell1.63e-15433
B cell5.59e-1514
Langerhans cell9.38e-135
conventional dendritic cell1.92e-128
plasmacytoid dendritic cell6.86e-083
basophil7.01e-083
single nucleate cell8.81e-083
mononuclear cell8.81e-083
somatic cell1.25e-07588
natural killer cell2.06e-073
pro-NK cell2.06e-073
Uber Anatomy
Ontology termp-valuen
bone marrow1.88e-4076
hematopoietic system1.33e-3798
blood island1.33e-3798
bone element1.29e-3682
hemolymphoid system1.78e-34108
immune system1.66e-3293
skeletal element2.69e-3290
skeletal system7.10e-28100
connective tissue1.88e-21371
lateral plate mesoderm2.41e-12203
musculoskeletal system3.96e-12167


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
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
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.12.3112
MA0051.11.58921
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.11.35477
MA0061.14.48545
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.11.51422
MA0072.12.29768
MA0073.13.48283
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.81721
MA0103.10.381434
MA0105.11.94389
MA0106.10.70837
MA0107.13.24579
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.11.96285
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
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
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.27.22997e-05
MA0102.21.58513
MA0258.10.289793
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
MEF2A#420539.371615454822030.002687399947103910.0148016750910023
NFKB1#479043.658708949462560.01207927289015230.0438295932103886
RFX5#599336.023955413597550.009437904036335060.0356022993444628
TBP#690853.088975572580320.006645448275786930.0282867611866201



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:C1389&oldid=3068506"