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Coexpression cluster:C3184: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.758317,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;1.59304,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;1.15625,MA0063.1;0,MA0066.1;2.1667,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;5.1975,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;1.70054,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;1.55117,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;1.52002,MA0105.1;0.846801,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.707589,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.757898,MA0138.2;1.04628,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;3.77966,MA0065.2;1.39232,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;2.02721,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;2.48891,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;2.70224,MA0102.2;1.88331,MA0258.1;2.22591,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:11, 22 January 2013


Full id: C3184_Eosinophils_CD8_CD4_Neutrophils_hairy_Whole_B



Phase1 CAGE Peaks

Hg19::chr11:64107589..64107604,-p@chr11:64107589..64107604
-
Hg19::chr19:6772686..6772697,+p2@VAV1
Hg19::chr22:24823517..24823546,+p5@ADORA2A


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
5.91277682223884e-050.03742787728477182220Signalling by NGF (Reactome):REACT_11061



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:0006909phagocytosis0.00025294983684129
GO:0010324membrane invagination0.00198514209351949
GO:0006897endocytosis0.00198514209351949
GO:0032230positive regulation of synaptic transmission, GABAergic0.00247927857153759
GO:0016044membrane organization and biogenesis0.00247927857153759
GO:0001973adenosine receptor signaling pathway0.00299401826913486
GO:0001611A2A adenosine receptor activity, G-protein coupled0.00299401826913486
GO:0032228regulation of synaptic transmission, GABAergic0.00349291848885374
GO:0042755eating behavior0.00349291848885374
GO:0051932synaptic transmission, GABAergic0.00349291848885374
GO:0001975response to amphetamine0.00349291848885374
GO:0014075response to amine stimulus0.00349291848885374
GO:0050790regulation of catalytic activity0.00366740246370577
GO:0016192vesicle-mediated transport0.00366740246370577
GO:0050806positive regulation of synaptic transmission0.00366740246370577
GO:0065009regulation of a molecular function0.00366740246370577
GO:0001609adenosine receptor activity, G-protein coupled0.00366740246370577
GO:0030676Rac guanyl-nucleotide exchange factor activity0.00366740246370577
GO:0051971positive regulation of transmission of nerve impulse0.00366740246370577
GO:0001963synaptic transmission, dopaminergic0.00366740246370577
GO:0031646positive regulation of neurological process0.00399167181551987
GO:0045785positive regulation of cell adhesion0.00714344921713767
GO:0050804regulation of synaptic transmission0.00728828147067584
GO:0051969regulation of transmission of nerve impulse0.00765586138917796
GO:0007270nerve-nerve synaptic transmission0.00765586138917796
GO:0006171cAMP biosynthetic process0.00765586138917796
GO:0046058cAMP metabolic process0.00851123181759712
GO:0007190adenylate cyclase activation0.00851123181759712
GO:0031644regulation of neurological process0.00851123181759712
GO:0045762positive regulation of adenylate cyclase activity0.00851123181759712
GO:0031281positive regulation of cyclase activity0.00851123181759712
GO:0051349positive regulation of lyase activity0.00851123181759712
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0109712805277906
GO:0007631feeding behavior0.0109712805277906
GO:0009190cyclic nucleotide biosynthetic process0.0109712805277906
GO:0045761regulation of adenylate cyclase activity0.0109712805277906
GO:0031279regulation of cyclase activity0.0109712805277906
GO:0051339regulation of lyase activity0.0109712805277906
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0109712805277906
GO:0001608nucleotide receptor activity, G-protein coupled0.0109712805277906
GO:0016502nucleotide receptor activity0.0109712805277906
GO:0001614purinergic nucleotide receptor activity0.0109712805277906
GO:0009187cyclic nucleotide metabolic process0.0121763494559456
GO:0007242intracellular signaling cascade0.0135282592478952
GO:0019992diacylglycerol binding0.0137276904705138
GO:0010033response to organic substance0.0141114826117002
GO:0030155regulation of cell adhesion0.0147014195766507
GO:0006968cellular defense response0.0157024009538919
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0175506373098121
GO:0007229integrin-mediated signaling pathway0.0175506373098121
GO:0019933cAMP-mediated signaling0.0175506373098121
GO:0007166cell surface receptor linked signal transduction0.0175506373098121
GO:0007596blood coagulation0.0197432993336674
GO:0050817coagulation0.019764653657151
GO:0007599hemostasis0.0199751569658774
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0218567002300837
GO:0019935cyclic-nucleotide-mediated signaling0.0223892589633975
GO:0050878regulation of body fluid levels0.0225433032418296
GO:0042060wound healing0.0232228968375412
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0262997025568311
GO:0016043cellular component organization and biogenesis0.0262997025568311
GO:0008015blood circulation0.0262997025568311
GO:0003013circulatory system process0.0262997025568311
GO:0035023regulation of Rho protein signal transduction0.0262997025568311
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0265368819590599
GO:0007626locomotory behavior0.0286623246375753
GO:0007266Rho protein signal transduction0.0293234423434123
GO:0043087regulation of GTPase activity0.0324158935762655
GO:0007417central nervous system development0.0355671701565904
GO:0006810transport0.0358650919401976
GO:0051234establishment of localization0.0366111125560204
GO:0009165nucleotide biosynthetic process0.0366111125560204
GO:0043085positive regulation of catalytic activity0.0366111125560204
GO:0019932second-messenger-mediated signaling0.0378026194446836
GO:0051239regulation of multicellular organismal process0.0385460220629078
GO:0007268synaptic transmission0.039193714268358
GO:0006954inflammatory response0.039193714268358
GO:0007610behavior0.039193714268358
GO:0051179localization0.039193714268358
GO:0051336regulation of hydrolase activity0.0397950531681832
GO:0005085guanyl-nucleotide exchange factor activity0.0397950531681832
GO:0019226transmission of nerve impulse0.0419682489221858
GO:0009117nucleotide metabolic process0.0427127318453849
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0455375661295008
GO:0046578regulation of Ras protein signal transduction0.0458554250684929
GO:0007165signal transduction0.0474101992469932



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
leukocyte1.88e-80136
hematopoietic stem cell7.17e-74168
angioblastic mesenchymal cell7.17e-74168
hematopoietic cell8.65e-73177
hematopoietic oligopotent progenitor cell6.50e-67161
hematopoietic multipotent progenitor cell6.50e-67161
nongranular leukocyte7.77e-65115
hematopoietic lineage restricted progenitor cell3.96e-60120
lymphocyte9.61e-5553
common lymphoid progenitor9.61e-5553
lymphoid lineage restricted progenitor cell6.36e-5452
nucleate cell5.23e-5255
T cell8.81e-2825
pro-T cell8.81e-2825
lymphocyte of B lineage1.47e-2324
pro-B cell1.47e-2324
mature alpha-beta T cell5.39e-2118
alpha-beta T cell5.39e-2118
immature T cell5.39e-2118
mature T cell5.39e-2118
immature alpha-beta T cell5.39e-2118
myeloid leukocyte1.12e-2072
myeloid cell5.67e-20108
common myeloid progenitor5.67e-20108
mesenchymal cell5.01e-16354
classical monocyte8.10e-1642
CD14-positive, CD16-negative classical monocyte8.10e-1642
connective tissue cell4.35e-15361
granulocyte monocyte progenitor cell3.20e-1467
CD8-positive, alpha-beta T cell5.21e-1411
macrophage dendritic cell progenitor6.97e-1461
defensive cell1.22e-1348
phagocyte1.22e-1348
monopoietic cell1.24e-1359
monocyte1.24e-1359
monoblast1.24e-1359
promonocyte1.24e-1359
myeloid lineage restricted progenitor cell1.39e-1366
B cell2.55e-1314
motile cell7.42e-12386
granulocyte5.03e-108
blood cell3.14e-0811
multi fate stem cell4.09e-08427
CD4-positive, alpha-beta T cell1.04e-076
somatic stem cell1.27e-07433
intermediate monocyte1.69e-079
CD14-positive, CD16-positive monocyte1.69e-079
stem cell2.37e-07441
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.60e-2898
blood island6.60e-2898
hemolymphoid system1.18e-24108
immune system3.68e-1593
connective tissue8.02e-14371
blood9.07e-1415
haemolymphatic fluid9.07e-1415
organism substance9.07e-1415
bone marrow8.24e-1376
bone element4.80e-1182
skeletal element4.19e-0990
hemopoietic organ1.43e-087
immune organ1.43e-087
skeletal system3.48e-07100
Disease
Ontology termp-valuen
lymphoma1.52e-1010
hematologic cancer1.13e-0951
immune system cancer1.13e-0951


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.15.1975
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.23.77966
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.12.48891
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
MA0102.21.88331
MA0258.12.22591
MA0259.10.575594
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
EBF1#187938.9064668465690.00141523283560980.0091260497726755
ELF1#199734.258097958807540.01295179875054610.0460265034437471
ZEB1#6935211.25895467836260.01010222676646330.0377983900427277



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:C3184&oldid=2571695"