Personal tools

Coexpression cluster:C446: 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 11:23, 17 September 2013


Full id: C446_Neutrophils_Mast_Eosinophils_Whole_CD14_immature_optic



Phase1 CAGE Peaks

Hg19::chr11:59521653..59521681,+p@chr11:59521653..59521681
+
Hg19::chr14:75746340..75746368,+p3@FOS
Hg19::chr14:93118094..93118129,+p8@RIN3
Hg19::chr14:93118130..93118140,+p18@RIN3
Hg19::chr16:27325997..27326036,+p@chr16:27325997..27326036
+
Hg19::chr17:3819751..3819767,-p1@P2RX1
Hg19::chr17:4802910..4802929,+p5@C17orf107
Hg19::chr1:231665876..231665886,-p@chr1:231665876..231665886
-
Hg19::chr1:231666076..231666093,+p@chr1:231666076..231666093
+
Hg19::chr20:34357224..34357250,+p@chr20:34357224..34357250
+
Hg19::chr2:208029288..208029307,+p@chr2:208029288..208029307
+
Hg19::chr2:232469321..232469404,-p@chr2:232469321..232469404
-
Hg19::chr2:43358229..43358245,-p@chr2:43358229..43358245
-
Hg19::chr2:43453036..43453081,-p@chr2:43453036..43453081
-
Hg19::chr2:43453083..43453099,-p@chr2:43453083..43453099
-
Hg19::chr4:141074616..141074637,-p7@MAML3
Hg19::chr4:160024275..160024320,+p@chr4:160024275..160024320
+
Hg19::chr4:160024323..160024354,+p@chr4:160024323..160024354
+
Hg19::chr4:160025300..160025318,+p9@RAPGEF2
Hg19::chr4:6918626..6918641,+p@chr4:6918626..6918641
+
Hg19::chr6:138188551..138188562,+p5@TNFAIP3
Hg19::chr7:28725740..28725778,+p1@CREB5


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:0005515protein binding0.0198265617681682
GO:0006366transcription from RNA polymerase II promoter0.0222516553977654
GO:0065007biological regulation0.0222516553977654
GO:0017034Rap guanyl-nucleotide exchange factor activity0.0222516553977654
GO:0046582Rap GTPase activator activity0.023800322236145
GO:0004931ATP-gated cation channel activity0.023800322236145
GO:0035249synaptic transmission, glutamatergic0.023800322236145
GO:0045893positive regulation of transcription, DNA-dependent0.023800322236145
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0265035690185179
GO:0007165signal transduction0.0265035690185179
GO:0045941positive regulation of transcription0.0265035690185179
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0265035690185179
GO:0007154cell communication0.0296771541767025
GO:0050794regulation of cellular process0.0296771541767025
GO:0005096GTPase activator activity0.0296771541767025
GO:0031325positive regulation of cellular metabolic process0.0296771541767025
GO:0046983protein dimerization activity0.0296771541767025
GO:0007243protein kinase cascade0.0296771541767025
GO:0009893positive regulation of metabolic process0.0303613989977837
GO:0050789regulation of biological process0.0315500390975979
GO:0006357regulation of transcription from RNA polymerase II promoter0.0320551948780199
GO:0042310vasoconstriction0.0323260544063619
GO:0044451nucleoplasm part0.0323557424108025
GO:0008047enzyme activator activity0.0323557424108025
GO:0007270nerve-nerve synaptic transmission0.0337717794615979
GO:0005654nucleoplasm0.0364885636811877
GO:0006305DNA alkylation0.0364885636811877
GO:0006306DNA methylation0.0364885636811877
GO:0006304DNA modification0.0428701763320134



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
classical monocyte9.80e-4842
CD14-positive, CD16-negative classical monocyte9.80e-4842
myeloid leukocyte6.81e-4672
defensive cell2.60e-4148
phagocyte2.60e-4148
leukocyte4.20e-39136
granulocyte monocyte progenitor cell1.86e-3767
myeloid lineage restricted progenitor cell8.81e-3566
macrophage dendritic cell progenitor5.43e-3361
monopoietic cell3.60e-3159
monocyte3.60e-3159
monoblast3.60e-3159
promonocyte3.60e-3159
hematopoietic stem cell4.22e-29168
angioblastic mesenchymal cell4.22e-29168
myeloid cell6.50e-29108
common myeloid progenitor6.50e-29108
hematopoietic lineage restricted progenitor cell7.46e-29120
hematopoietic cell3.38e-26177
nongranular leukocyte3.95e-26115
hematopoietic oligopotent progenitor cell4.08e-26161
hematopoietic multipotent progenitor cell4.08e-26161
stuff accumulating cell2.64e-1787
granulocyte2.12e-118
intermediate monocyte4.14e-119
CD14-positive, CD16-positive monocyte4.14e-119
blood cell1.26e-0711
histamine secreting cell3.83e-075
biogenic amine secreting cell3.83e-075
granulocytopoietic cell3.83e-075
mast cell3.83e-075
mast cell progenitor3.83e-075
basophil mast progenitor cell3.83e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.42e-4298
blood island2.42e-4298
hemolymphoid system1.13e-38108
bone marrow2.24e-3376
immune system9.84e-3193
bone element1.63e-2982
skeletal element3.35e-2590
adult organism1.36e-22114
skeletal system7.79e-21100
lateral plate mesoderm4.37e-15203
blood1.00e-0815
haemolymphatic fluid1.00e-0815
organism substance1.00e-0815
musculoskeletal system5.07e-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)
MA0003.10.762126
MA0004.10.478761
MA0006.10.244486
MA0007.11.41691
MA0009.10.526253
MA0014.11.16359
MA0017.10.297619
MA0019.10.262545
MA0024.11.10823
MA0025.10.647545
MA0027.12.09389
MA0028.10.562332
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.10.456051
MA0041.13.76855
MA0042.13.53324
MA0043.10.526535
MA0046.10.516541
MA0048.11.0794
MA0050.10.458935
MA0051.10.22589
MA0052.10.459414
MA0055.10.45605
MA0056.10
MA0057.10.748244
MA0058.11.12955
MA0059.10.101051
MA0060.10.109486
MA0061.15.91004
MA0063.10
MA0066.10.649177
MA0067.10.820123
MA0068.11.10491
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.10.260075
MA0074.10.225345
MA0076.10.110503
MA0077.10.49237
MA0078.10.814281
MA0081.10.331815
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.11.1154
MA0089.10
MA0090.10.378129
MA0091.10.482932
MA0092.10.136418
MA0093.10.906091
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.12.49553
MA0103.10.232452
MA0105.15.44873
MA0106.10.259598
MA0107.13.08202
MA0108.20.383574
MA0109.10
MA0111.10.398557
MA0113.10.272101
MA0114.10.358913
MA0115.10.747865
MA0116.11.4789
MA0117.10.560027
MA0119.10.308642
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.660517
MA0139.10.37546
MA0140.10.199454
MA0141.10.329072
MA0142.10.359701
MA0143.11.37255
MA0144.10.140794
MA0145.11.23864
MA0146.10.485361
MA0147.10.0444528
MA0148.10.174705
MA0149.10.192747
MA0062.20.396181
MA0035.20.198962
MA0039.21.06886
MA0138.20.302079
MA0002.21.49131
MA0137.20.274591
MA0104.20.0256869
MA0047.20.250458
MA0112.22.19584
MA0065.20.502939
MA0150.10.369323
MA0151.10
MA0152.10.20405
MA0153.10.615584
MA0154.10.650439
MA0155.10.609284
MA0156.10.0812668
MA0157.10.337287
MA0158.10
MA0159.10.386598
MA0160.10.543697
MA0161.10
MA0162.11.3611
MA0163.12.02048
MA0164.10.28168
MA0080.20.531199
MA0018.20.722038
MA0099.20.59018
MA0079.23.05238
MA0102.21.03595
MA0258.10.892318
MA0259.10.0476147
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
BCL3#60246.281291418861510.0033780447209390.017250971229287
CEBPB#105193.260924028746520.000816954709745570.00622424372126623
EBF1#187993.643554619050960.0003565182731096630.00356753970732012
EGR1#1958102.267354134004610.006246180724458260.0275634794727552
FOS#235372.862985780102770.007857022262011480.0322643631511114
FOSL2#235553.847772864673110.008111181980340430.0320346292105874
GATA2#262463.475890472787450.005791119096792690.0260372244758678
JUN#372584.550119706304120.0001907444499628440.00230542293827907
MAX#414982.346383821457140.01378982480437180.0485110318224126
POLR2A#5430191.854618652481970.0001323508483376390.00173956585068395
SMARCA4#6597214.25144575526250.008629299868192340.0328714100351657
SMARCB1#659854.148344495717590.005924604685930550.0265721802282015
SMARCC1#659947.938792603569360.001444440010927480.00926234851729937
SMARCC2#6601312.83936924003150.00158400214699310.00998259716568986
SPI1#6688103.729237958419420.0001152372266473390.00157612109924325
TCF12#693873.383693377968410.003100341367112750.016302313565597
ZNF263#1012772.616040520867030.01273640958752610.0459410748398026



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:C446&oldid=3067563"