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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,0

Latest revision as of 11:25, 17 September 2013


Full id: C560_Neutrophils_Eosinophils_CD14CD16_Whole_CD14_acute_Dendritic



Phase1 CAGE Peaks

Hg19::chr11:3862154..3862165,-p3@RHOG
Hg19::chr15:40600066..40600089,-p3@PLCB2
Hg19::chr16:3137080..3137121,-p@chr16:3137080..3137121
-
Hg19::chr19:2282186..2282208,-p1@C19orf35
Hg19::chr19:48753064..48753095,-p1@CARD8
Hg19::chr1:161039493..161039519,-p3@ARHGAP30
Hg19::chr1:161039535..161039544,-p11@ARHGAP30
Hg19::chr20:62708698..62708701,+p@chr20:62708698..62708701
+
Hg19::chr20:62710832..62710879,-p1@RGS19
Hg19::chr20:62710880..62710898,-p3@RGS19
Hg19::chr20:62711425..62711470,+p2@OPRL1
Hg19::chr22:40859415..40859478,-p2@MKL1
Hg19::chr2:220042536..220042549,-p5@CNPPD1
Hg19::chr6:31554456..31554512,+p6@LST1
Hg19::chrX:109245878..109245916,+p2@TMEM164
Hg19::chrX:77583054..77583100,-p1@CYSLTR1


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

p.valueFDRnGenesnPathwayName
1.43919346767955e-050.009110094650411545932Signaling by GPCR (Reactome):REACT_14797
0.0001232194972615820.03899897088329064733{ARRB2,743} (Static Module):NA



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:0065007biological regulation0.00768606826536886
GO:0007242intracellular signaling cascade0.00768606826536886
GO:0007165signal transduction0.00768606826536886
GO:0051480cytosolic calcium ion homeostasis0.00768606826536886
GO:0007204elevation of cytosolic calcium ion concentration0.00768606826536886
GO:0051345positive regulation of hydrolase activity0.00768606826536886
GO:0007154cell communication0.00768606826536886
GO:0008047enzyme activator activity0.00768606826536886
GO:0032089NACHT domain binding0.00768606826536886
GO:0009968negative regulation of signal transduction0.00963686219868977
GO:0006874cellular calcium ion homeostasis0.00963686219868977
GO:0055074calcium ion homeostasis0.00963686219868977
GO:0006875cellular metal ion homeostasis0.00963686219868977
GO:0055065metal ion homeostasis0.00963686219868977
GO:0007186G-protein coupled receptor protein signaling pathway0.0153133997986742
GO:0015051X-opioid receptor activity0.0164799494906198
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0164799494906198
GO:0055066di-, tri-valent inorganic cation homeostasis0.0164799494906198
GO:0004974leukotriene receptor activity0.0173368271137648
GO:0030003cellular cation homeostasis0.0173368271137648
GO:0055080cation homeostasis0.0173368271137648
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0188533124660523
GO:0055082cellular chemical homeostasis0.0202857552107383
GO:0006873cellular ion homeostasis0.0202857552107383
GO:0050718positive regulation of interleukin-1 beta secretion0.0202857552107383
GO:0050706regulation of interleukin-1 beta secretion0.0202857552107383
GO:0043085positive regulation of catalytic activity0.0202857552107383
GO:0050716positive regulation of interleukin-1 secretion0.0202857552107383
GO:0050704regulation of interleukin-1 secretion0.0202857552107383
GO:0050801ion homeostasis0.0202857552107383
GO:0019932second-messenger-mediated signaling0.0202857552107383
GO:0050702interleukin-1 beta secretion0.0215913114519548
GO:0050672negative regulation of lymphocyte proliferation0.0217118145535234
GO:0032945negative regulation of mononuclear cell proliferation0.0217118145535234
GO:0050701interleukin-1 secretion0.0217118145535234
GO:0048878chemical homeostasis0.021812809706439
GO:0051336regulation of hydrolase activity0.021812809706439
GO:0016358dendrite development0.021812809706439
GO:0048523negative regulation of cellular process0.0222381094285401
GO:0050715positive regulation of cytokine secretion0.0222381094285401
GO:0007166cell surface receptor linked signal transduction0.0222381094285401
GO:0004985opioid receptor activity0.0224114206445887
GO:0008656caspase activator activity0.0224114206445887
GO:0048519negative regulation of biological process0.0224114206445887
GO:0005096GTPase activator activity0.0225427971115012
GO:0050707regulation of cytokine secretion0.0225427971115012
GO:0007202phospholipase C activation0.0225427971115012
GO:0050714positive regulation of protein secretion0.0225427971115012
GO:0016505apoptotic protease activator activity0.0225427971115012
GO:0019725cellular homeostasis0.0238912041264944
GO:0016504protease activator activity0.0238912041264944
GO:0007193G-protein signaling, adenylate cyclase inhibiting pathway0.0238912041264944
GO:0051250negative regulation of lymphocyte activation0.024739396424922
GO:0050663cytokine secretion0.0255558362491887
GO:0043028caspase regulator activity0.0258718582086354
GO:0051047positive regulation of secretion0.0258718582086354
GO:0006914autophagy0.0309068112179078
GO:0050708regulation of protein secretion0.0309068112179078
GO:0042127regulation of cell proliferation0.031677914247718
GO:0042592homeostatic process0.0325735113717887
GO:0007585respiratory gaseous exchange0.032764573503621
GO:0005834heterotrimeric G-protein complex0.0410853019415701
GO:0022603regulation of anatomical structure morphogenesis0.0431284191752502
GO:0022604regulation of cell morphogenesis0.0431284191752502
GO:0050670regulation of lymphocyte proliferation0.0431284191752502
GO:0032944regulation of mononuclear cell proliferation0.0431284191752502
GO:0008360regulation of cell shape0.0431284191752502
GO:0050790regulation of catalytic activity0.0442110780729895
GO:0004435phosphoinositide phospholipase C activity0.0442110780729895
GO:0004434inositol or phosphatidylinositol phosphodiesterase activity0.0442110780729895
GO:0019897extrinsic to plasma membrane0.0477272926776687
GO:0043280positive regulation of caspase activity0.0477272926776687
GO:0032943mononuclear cell proliferation0.048449248386039
GO:0046651lymphocyte proliferation0.048449248386039
GO:0065009regulation of a molecular function0.048449248386039
GO:0050794regulation of cellular process0.048449248386039
GO:0005624membrane fraction0.048449248386039
GO:0004629phospholipase C activity0.048449248386039
GO:0009306protein secretion0.048449248386039
GO:0005794Golgi apparatus0.048449248386039
GO:0030695GTPase regulator activity0.048449248386039
GO:0051046regulation of secretion0.048449248386039
GO:0004871signal transducer activity0.048449248386039
GO:0060089molecular transducer activity0.048449248386039
GO:0043281regulation of caspase activity0.048449248386039



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell1.24e-84168
angioblastic mesenchymal cell1.24e-84168
hematopoietic oligopotent progenitor cell1.44e-80161
hematopoietic multipotent progenitor cell1.44e-80161
hematopoietic cell3.97e-77177
leukocyte7.03e-72136
myeloid cell4.77e-64108
common myeloid progenitor4.77e-64108
hematopoietic lineage restricted progenitor cell9.15e-61120
nongranular leukocyte3.25e-58115
myeloid leukocyte1.32e-5372
granulocyte monocyte progenitor cell1.01e-4767
myeloid lineage restricted progenitor cell1.13e-4666
macrophage dendritic cell progenitor2.11e-4361
monopoietic cell1.53e-4259
monocyte1.53e-4259
monoblast1.53e-4259
promonocyte1.53e-4259
defensive cell2.06e-3748
phagocyte2.06e-3748
classical monocyte1.08e-3242
CD14-positive, CD16-negative classical monocyte1.08e-3242
nucleate cell4.55e-1555
lymphocyte1.69e-1453
common lymphoid progenitor1.69e-1453
lymphoid lineage restricted progenitor cell3.08e-1452
mesenchymal cell6.84e-13354
stuff accumulating cell7.11e-1287
connective tissue cell8.47e-12361
mature alpha-beta T cell5.33e-1018
alpha-beta T cell5.33e-1018
immature T cell5.33e-1018
mature T cell5.33e-1018
immature alpha-beta T cell5.33e-1018
intermediate monocyte3.89e-099
CD14-positive, CD16-positive monocyte3.89e-099
granulocyte2.20e-088
motile cell3.57e-08386
lymphocyte of B lineage2.46e-0724
pro-B cell2.46e-0724
CD8-positive, alpha-beta T cell4.22e-0711
T cell7.97e-0725
pro-T cell7.97e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.85e-5398
blood island5.85e-5398
hemolymphoid system3.59e-49108
bone marrow5.23e-4176
immune system1.00e-4093
bone element8.88e-3682
skeletal element5.74e-3090
skeletal system7.99e-25100
adult organism1.67e-20114
lateral plate mesoderm5.10e-15203
connective tissue9.79e-11371
blood8.70e-0915
haemolymphatic fluid8.70e-0915
organism substance8.70e-0915
musculoskeletal system3.19e-07167
Disease
Ontology termp-valuen
myeloid leukemia7.34e-1131
leukemia7.25e-0939
hematologic cancer6.93e-0851
immune system cancer6.93e-0851


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)
MA0003.13.4432
MA0004.10.670242
MA0006.10.392773
MA0007.10.636564
MA0009.10.644692
MA0014.13.42157
MA0017.10.89607
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.11.34419
MA0029.10.565022
MA0030.10.554453
MA0031.11.23979
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.643709
MA0050.10.647665
MA0051.10.851441
MA0052.10.574006
MA0055.13.20932
MA0056.10
MA0057.11.27784
MA0058.10.167587
MA0059.10.964661
MA0060.10.212419
MA0061.10.395503
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.10.303278
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.14.1014
MA0074.10.316991
MA0076.10.528959
MA0077.10.608956
MA0078.10.402443
MA0081.10.965129
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.20753
MA0089.10
MA0090.10.189305
MA0091.10.674976
MA0092.10.607109
MA0093.10.793328
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.802624
MA0103.10.118522
MA0105.10.16519
MA0106.10.355999
MA0107.10.285979
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.10.278245
MA0115.10.874839
MA0116.15.70333
MA0117.10.680135
MA0119.10.471628
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.12.38342
MA0139.11.93105
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.0738381
MA0145.11.26426
MA0146.12.3754
MA0147.10.617362
MA0148.10.257816
MA0149.10.279141
MA0062.23.13955
MA0035.20.286421
MA0039.25.35067
MA0138.20.403517
MA0002.21.16356
MA0137.20.138998
MA0104.20.462925
MA0047.20.345656
MA0112.21.56287
MA0065.21.66996
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.13.46847
MA0155.11.88309
MA0156.12.67491
MA0157.11.1256
MA0158.10
MA0159.10.29763
MA0160.10.26995
MA0161.10
MA0162.12.09948
MA0163.11.99493
MA0164.10.99163
MA0080.24.84521
MA0018.20.357181
MA0099.20.292649
MA0079.215.8408
MA0102.21.16862
MA0258.10.890751
MA0259.10.309645
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
EGR1#195882.494089547405070.0071065613147760.0296288286288978
ELF1#1997123.193573469105651.93117413800973e-050.000435803577786514
MAX#414972.822993035190620.00671495219734910.0285442180202264
POLR2A#5430152.013237353023199.45926752373161e-050.00137115397766968
SPI1#6688136.666012850674725.10515875363416e-104.93226341416094e-08
ZEB1#693544.222108004385960.01258112314888720.0454956518315372



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:C560&oldid=3067677"