Personal tools

Coexpression cluster:C627: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(2 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 11:27, 17 September 2013


Full id: C627_Mast_Eosinophils_CD14_Neutrophils_Basophils_immature_CD19



Phase1 CAGE Peaks

Hg19::chr12:76477834..76477866,+p@chr12:76477834..76477866
+
Hg19::chr13:31191097..31191149,-p@chr13:31191097..31191149
-
Hg19::chr13:31191229..31191249,+p@chr13:31191229..31191249
+
Hg19::chr14:35874296..35874308,-p12@NFKBIA
Hg19::chr17:4802892..4802907,+p6@C17orf107
Hg19::chr17:62972127..62972155,-p3@AMZ2P1
Hg19::chr17:81147692..81147717,-p@chr17:81147692..81147717
-
Hg19::chr1:159895503..159895508,+p@chr1:159895503..159895508
+
Hg19::chr22:37638755..37638764,+p@chr22:37638755..37638764
+
Hg19::chr2:208394286..208394306,-p@chr2:208394286..208394306
-
Hg19::chr5:56469337..56469348,-p@chr5:56469337..56469348
-
Hg19::chr5:56469358..56469387,-p@chr5:56469358..56469387
-
Hg19::chr5:56469388..56469429,-p@chr5:56469388..56469429
-
Hg19::chr7:140624061..140624074,-p@chr7:140624061..140624074
-


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:0045746negative regulation of Notch signaling pathway0.00210173083716001
GO:0043330response to exogenous dsRNA0.00210173083716001
GO:0008593regulation of Notch signaling pathway0.00210173083716001
GO:0007253cytoplasmic sequestering of NF-kappaB0.00210173083716001
GO:0042347negative regulation of NF-kappaB import into nucleus0.00210173083716001
GO:0031663lipopolysaccharide-mediated signaling pathway0.00210173083716001
GO:0032496response to lipopolysaccharide0.00210173083716001
GO:0043331response to dsRNA0.00210173083716001
GO:0043392negative regulation of DNA binding0.00210173083716001
GO:0051100negative regulation of binding0.00210173083716001
GO:0008139nuclear localization sequence binding0.00210173083716001
GO:0042994cytoplasmic sequestering of transcription factor0.00210173083716001
GO:0051220cytoplasmic sequestering of protein0.00210173083716001
GO:0002237response to molecule of bacterial origin0.00210173083716001
GO:0042308negative regulation of protein import into nucleus0.00210173083716001
GO:0042992negative regulation of transcription factor import into nucleus0.00210173083716001
GO:0051101regulation of DNA binding0.00210173083716001
GO:0042345regulation of NF-kappaB import into nucleus0.00210173083716001
GO:0042348NF-kappaB import into nucleus0.00210173083716001
GO:0046823negative regulation of nucleocytoplasmic transport0.00210173083716001
GO:0051224negative regulation of protein transport0.00216845245103811
GO:0051059NF-kappaB binding0.00256878213430668
GO:0045638negative regulation of myeloid cell differentiation0.00256878213430668
GO:0031625ubiquitin protein ligase binding0.00256878213430668
GO:0042990regulation of transcription factor import into nucleus0.00256878213430668
GO:0005048signal sequence binding0.00256878213430668
GO:0042991transcription factor import into nucleus0.00256878213430668
GO:0033157regulation of intracellular protein transport0.00256878213430668
GO:0000060protein import into nucleus, translocation0.00256878213430668
GO:0042306regulation of protein import into nucleus0.00256878213430668
GO:0032507maintenance of cellular protein localization0.00265370055196971
GO:0051651maintenance of cellular localization0.00265370055196971
GO:0032386regulation of intracellular transport0.00265370055196971
GO:0045185maintenance of protein localization0.00267867655716472
GO:0051223regulation of protein transport0.00272446590002224
GO:0051098regulation of binding0.00272446590002224
GO:0046822regulation of nucleocytoplasmic transport0.00274550424674056
GO:0051051negative regulation of transport0.00285761648912107
GO:0045637regulation of myeloid cell differentiation0.00305379694288207
GO:0051235maintenance of localization0.00359045684681502
GO:0007219Notch signaling pathway0.00427181064463418
GO:0045596negative regulation of cell differentiation0.00542113112759527
GO:0030099myeloid cell differentiation0.00613004827505004
GO:0051093negative regulation of developmental process0.00613004827505004
GO:0006606protein import into nucleus0.00746266746527831
GO:0051170nuclear import0.00746266746527831
GO:0009968negative regulation of signal transduction0.00773553710899171
GO:0009617response to bacterium0.00773553710899171
GO:0051049regulation of transport0.00786361877848985
GO:0017038protein import0.00854703873778406
GO:0007249I-kappaB kinase/NF-kappaB cascade0.00954707798579222
GO:0045595regulation of cell differentiation0.00970029617150775
GO:0006913nucleocytoplasmic transport0.0101194447715112
GO:0051169nuclear transport0.0101194447715112
GO:0030097hemopoiesis0.010253898932811
GO:0048534hemopoietic or lymphoid organ development0.0108214117508536
GO:0002520immune system development0.0111846494843018
GO:0051707response to other organism0.0123491529415052
GO:0042277peptide binding0.0123491529415052
GO:0006605protein targeting0.0127271478472467
GO:0050793regulation of developmental process0.0135521441958952
GO:0009607response to biotic stimulus0.0163279626865388
GO:0019899enzyme binding0.016958410194016
GO:0051704multi-organism process0.018225947103497
GO:0042802identical protein binding0.0196161544801601
GO:0007243protein kinase cascade0.0199558281508122
GO:0008134transcription factor binding0.022585764220227
GO:0042127regulation of cell proliferation0.0241596020251972
GO:0006886intracellular protein transport0.0268554495859335
GO:0005829cytosol0.0284234075120688
GO:0042221response to chemical stimulus0.0290591423259917
GO:0065009regulation of a molecular function0.0326449396234808
GO:0008283cell proliferation0.0357486181206441
GO:0009966regulation of signal transduction0.0378690240929732
GO:0006915apoptosis0.0393960801943847
GO:0012501programmed cell death0.0393960801943847
GO:0015031protein transport0.0393960801943847
GO:0016265death0.0398453137878252
GO:0008219cell death0.0398453137878252
GO:0046907intracellular transport0.0398453137878252
GO:0045184establishment of protein localization0.0398723422193731
GO:0008104protein localization0.0410521002949344
GO:0033036macromolecule localization0.0427098716306413
GO:0051649establishment of cellular localization0.0457877075238432
GO:0051641cellular localization0.045940131900375
GO:0048523negative regulation of cellular process0.045940131900375
GO:0048513organ development0.045940131900375
GO:0048519negative regulation of biological process0.047050110786423
GO:0048468cell development0.0488829531788902



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
leukocyte1.54e-62136
hematopoietic lineage restricted progenitor cell9.11e-50120
nongranular leukocyte3.59e-46115
hematopoietic stem cell7.56e-46168
angioblastic mesenchymal cell7.56e-46168
hematopoietic cell1.82e-45177
hematopoietic oligopotent progenitor cell2.35e-43161
hematopoietic multipotent progenitor cell2.35e-43161
classical monocyte2.90e-4342
CD14-positive, CD16-negative classical monocyte2.90e-4342
myeloid leukocyte5.42e-4372
defensive cell7.01e-3648
phagocyte7.01e-3648
granulocyte monocyte progenitor cell4.26e-3567
myeloid lineage restricted progenitor cell4.80e-3266
macrophage dendritic cell progenitor9.67e-3161
monopoietic cell1.71e-2859
monocyte1.71e-2859
monoblast1.71e-2859
promonocyte1.71e-2859
myeloid cell4.89e-27108
common myeloid progenitor4.89e-27108
stuff accumulating cell4.52e-1887
lymphoid lineage restricted progenitor cell4.98e-1552
lymphocyte1.49e-1453
common lymphoid progenitor1.49e-1453
nucleate cell1.16e-1355
intermediate monocyte3.58e-129
CD14-positive, CD16-positive monocyte3.58e-129
granulocyte1.17e-118
mesenchymal cell3.85e-10354
blood cell7.88e-1011
connective tissue cell1.93e-09361
CD4-positive, alpha-beta T cell7.38e-086
motile cell9.84e-08386
T cell1.75e-0725
pro-T cell1.75e-0725
circulating cell2.11e-076
histamine secreting cell4.77e-075
biogenic amine secreting cell4.77e-075
granulocytopoietic cell4.77e-075
mast cell4.77e-075
mast cell progenitor4.77e-075
basophil mast progenitor cell4.77e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.01e-3398
blood island6.01e-3398
bone marrow1.01e-3176
hemolymphoid system5.92e-30108
immune system1.81e-2993
bone element4.42e-2882
skeletal element5.15e-2490
skeletal system6.77e-20100
connective tissue7.20e-09371
lateral plate mesoderm3.78e-08203
musculoskeletal system8.09e-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)
MA0003.10.73459
MA0004.10.275994
MA0006.10.464315
MA0007.10.7221
MA0009.10.695988
MA0014.10.636453
MA0017.11.61959
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.492785
MA0029.10.614815
MA0030.11.4696
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.792277
MA0042.11.34583
MA0043.10.69629
MA0046.10.685589
MA0048.12.05724
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.12.82565
MA0056.10
MA0057.10.769632
MA0058.10.200063
MA0059.10.199079
MA0060.10.266757
MA0061.113.1639
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.11.49957
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.385259
MA0074.10.943486
MA0076.10.212295
MA0077.11.58596
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.752017
MA0089.10
MA0090.10.635809
MA0091.10.278153
MA0092.10.247341
MA0093.10.469677
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.18.2402
MA0103.10.146091
MA0105.18.26613
MA0106.10.399649
MA0107.113.1649
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.11.14609
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.453946
MA0140.10.327488
MA0141.10.574537
MA0142.10.514195
MA0143.10.414436
MA0144.10.316332
MA0145.10.324645
MA0146.10.74748
MA0147.10.72854
MA0148.10.296708
MA0149.10.319221
MA0062.20.473181
MA0035.20.872194
MA0039.21.52568
MA0138.20.44894
MA0002.20.531015
MA0137.20.168782
MA0104.20.952142
MA0047.21.00935
MA0112.20.78415
MA0065.20.846317
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.687815
MA0155.11.41283
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.361202
MA0160.10.30953
MA0161.10
MA0162.10.887082
MA0163.13.32868
MA0164.10.425415
MA0080.20.46983
MA0018.22.73684
MA0099.20.333432
MA0079.25.90757
MA0102.21.22472
MA0258.10.624652
MA0259.10.117259
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
BCL11A#53335510.13194825128828.32782329868578e-050.00125107816094857
BCL3#602717.27355140186924.86650874441473e-083.15098144301259e-06
CTCF#1066472.680128186537510.00785487248801420.0322580719506003
EBF1#187985.089409626610864.04144399024511e-050.000739979608866075
EGR1#195872.494089547405070.01176051944619070.042859128007562
HEY1#23462113.17437296244023.59719932856811e-050.000696492214824481
HMGN3#932463.505091881435970.004171546858416660.0198710231400765
HSF1#3297335.20514285714297.78651961638345e-050.00119996506155448
MEF2A#420545.355208831326870.005261339689734130.0243719088022773
MEF2C#420838.85243310556230.004223653285903120.0201045588408202
MXI1#460153.557704153128320.009377823043300660.0353884398330422
NANOG#7992336.266738245931280.01096023079276290.0403239350324221
NFKB1#4790103.92004530299561.9593663942264e-050.000438752716223438
PAX5#507994.287577841471463.71976426636989e-050.000718226031087826
PBX3#509046.261289339069750.002998943887654680.0159400834995556
POLR2A#5430121.840674151335490.003085141629167310.0162616890384882
POU2F2#545263.902624596175370.002402860079088870.013551072077324
SIN3A#2594272.704442363407570.007462461905995410.0307808870063292
TAF1#6872112.626679224514160.0002393683783156760.00260600375929437
TAL1#688648.533890479268630.0009593055636367060.00690196429874993
TBP#6908102.647693347925990.0006665529662652810.00544839361695075
TCF12#693864.557627815222750.001064276279763110.00751941214870648
THAP1#5514536.721959557753860.009053120490315810.034268379213805
ZBTB7A#5134163.150818274803960.007127639788689380.0296350798953354



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:C627&oldid=3067744"