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Coexpression cluster:C481: Difference between revisions

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{{Coexpression_clusters
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response!0.000145883258857863!6614;6366;6363$GO:0009611!response to wounding!0.000224102063886895!6614;6366;6363$GO:0006952!defense response!0.000298296102949237!6614;6366;6363$GO:0009605!response to external stimulus!0.000298296102949237!6614;6366;6363$GO:0008009!chemokine activity!0.000298296102949237!6366;6363$GO:0042379!chemokine receptor binding!0.000298296102949237!6366;6363$GO:0001664!G-protein-coupled receptor binding!0.000467526340171569!6366;6363$GO:0042330!taxis!0.000697921044060905!6366;6363$GO:0006935!chemotaxis!0.000697921044060905!6366;6363$GO:0006955!immune response!0.000888594413708518!3500;6366;6363$GO:0007626!locomotory behavior!0.000888594413708518!6366;6363$GO:0006950!response to stress!0.000888594413708518!6614;6366;6363$GO:0002376!immune system process!0.00119268236723501!3500;6366;6363$GO:0007610!behavior!0.00186582398897099!6366;6363$GO:0005125!cytokine activity!0.00193525642725649!6366;6363$GO:0005615!extracellular space!0.00522505994912853!6366;6363$GO:0042221!response to chemical stimulus!0.0061060531140756!6366;6363$GO:0044421!extracellular region part!0.013598993597661!6366;6363$GO:0005515!protein binding!0.0153227288807027!3500;6614;6366;6363$GO:0005102!receptor binding!0.015815430263547!6366;6363$GO:0009615!response to virus!0.0309701819201496!6363$GO:0007160!cell-matrix adhesion!0.0309701819201496!6614$GO:0031589!cell-substrate adhesion!0.0309701819201496!6614$GO:0006874!cellular calcium ion homeostasis!0.031476901111509!6363$GO:0055074!calcium ion homeostasis!0.031476901111509!6363$GO:0006875!cellular metal ion homeostasis!0.031476901111509!6363$GO:0055065!metal ion homeostasis!0.031476901111509!6363$GO:0003823!antigen binding!0.0420367370657912!3500$GO:0030005!cellular di-, tri-valent inorganic cation homeostasis!0.0420367370657912!6363$GO:0055066!di-, tri-valent inorganic cation homeostasis!0.0420367370657912!6363$GO:0030003!cellular cation 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1835,0.382614,0.128301,0.698586,0.504544,0.480558,0.741416,0.818365,0.78836,0.489274,0.450622,0.720898,0.357416,0.684379,0.878729,0.388459,0.351337,0.508343,0.813294,0.724739,0.680422,0.0815658,0.856695,0.785067,0.574613|tfbs_overrepresentation_for_novel_motifs=0.111472,1.88636,0.707844,0.19904,0.287896,0.197892,0.704649,0.324098,0.580675,0.13723,0.177199,0.286323,1.05698,0.684702,0.0842592,0.319274,0.43322,0.468601,0.481763,1.04122,0.348289,2.25678,0.561949,0.0823774,0.417677,0.304148,2.16714,0.558352,0.0865304,0.844228,0.489389,0.465029,1.07643,1.91555,0.240789,0.431552,0.0667305,0.1987,1.20345,0.117466,0.513665,0.904491,2.05487,0.594631,3.09268,0.125045,0.253928,0.507207,1.92831,0.609855,0.846555,0.727101,1.2317,0.532773,0.671855,0.68978,0.0887806,0.222594,1.18142,0.221865,0.500944,0.255713,0.582321,0.409576,0.269358,0.380605,0.754286,1.10771,0.456006,0.950487,0.143869,0.144782,0.036434,0.670004,0.224282,0.6434,1.6253,0.395294,2.00494,0.811071,0.497004,0.408665,0.269087,0.598548,0.622646,0.0608845,0.315868,1.52663,0.336397,1.20481,0.84263,0.598,0.4797,0.182928,0.0853298,0.0539379,0.103727,0.517267,0.340143,0.00964183,0.794596,0.474756,0.512318,0.436368,0.371019,0.517502,1.08332,0.241933,0.133935,0.0770225,0.364924,0.509866,0.693651,0.183573,0.797061,0.86793,0.159682,0.161925,0.378653,0.0497592,0.662347,0.889041,0.195973,0.277756,0.90249,0.395934,0.248345,0.484077,2.81391,0.054333,0.598629,0.164582,0.715286,0.275188,0.854902,0.148502,0.158817,0.191402,0.814541,1.65405,1.25623,0.779227,0.249639,0.514137,0.372477,0.216494,0.35869,1.49614,0.457994,0.0473483,0.197863,0.00178079,0.598976,0.554332,0.709821,0.980005,0.32333,1.97791,1.34035,0.116987,0.77808,0.582159,0.452507,0.760235,0.385896,0.268483,0.668756,2.00557,0.0689247|tfbs_overrepresentation_jaspar=MA0003.1;0.0152062,MA0004.1;0.180726,MA0006.1;0.597254,MA0007.1;0.502605,MA0009.1;0.561062,MA0014.1;0.0390946,MA0017.1;2.97266,MA0019.1;0.290278,MA0024.1;0.467291,MA0025.1;0.684106,MA0027.1;2.13512,MA0028.1;0.0924235,MA0029.1;0.484339,MA0030.1;0.474212,MA0031.1;0.41796,MA0038.1;0.709504,MA0040.1;0.489524,MA0041.1;0.193578,MA0042.1;0.171628,MA0043.1;0.561349,MA0046.1;0.551181,MA0048.1;0.418238,MA0050.1;0.512765,MA0051.1;0.251994,MA0052.1;0.492957,MA0055.1;1.94281,MA0056.1;0,MA0057.1;0.224163,MA0058.1;0.119655,MA0059.1;0.118893,MA0060.1;0.136253,MA0061.1;0.107862,MA0063.1;0,MA0066.1;3.70517,MA0067.1;0.858361,MA0068.1;0.0731654,MA0069.1;2.3178,MA0070.1;0.537571,MA0071.1;0.641904,MA0072.1;0.533514,MA0073.1;0.00109971,MA0074.1;0.251422,MA0076.1;0.129195,MA0077.1;0.526569,MA0078.1;0.33032,MA0081.1;0.37884,MA0083.1;0.567893,MA0084.1;1.03923,MA0087.1;0.531309,MA0088.1;0.107101,MA0089.1;0,MA0090.1;1.36506,MA0091.1;0.537838,MA0092.1;0.925428,MA0093.1;0.0855877,MA0095.1;0,MA0098.1;0,MA0100.1;0.265855,MA0101.1;0.0872967,MA0103.1;0.970204,MA0105.1;0.0885831,MA0106.1;0.782788,MA0107.1;0.195292,MA0108.2;1.06707,MA0109.1;0,MA0111.1;0.146643,MA0113.1;0.300221,MA0114.1;3.98453,MA0115.1;1.84688,MA0116.1;2.77299,MA0117.1;0.595385,MA0119.1;0.718217,MA0122.1;0.619196,MA0124.1;0.746208,MA0125.1;0.667416,MA0130.1;0,MA0131.1;0.345226,MA0132.1;0,MA0133.1;0,MA0135.1;0.588754,MA0136.1;0.260607,MA0139.1;0.0959198,MA0140.1;0.224213,MA0141.1;0.375925,MA0142.1;0.39079,MA0143.1;0.300362,MA0144.1;0.171577,MA0145.1;0.85225,MA0146.1;1.79544,MA0147.1;0.0556388,MA0148.1;0.198049,MA0149.1;0.21714,MA0062.2;0.0239298,MA0035.2;0.223695,MA0039.2;0.0406231,MA0138.2;0.882113,MA0002.2;0.123692,MA0137.2;0.0959012,MA0104.2;0.135419,MA0047.2;0.277681,MA0112.2;4.46229,MA0065.2;4.16035,MA0150.1;1.94158,MA0151.1;0,MA0152.1;0.648673,MA0153.1;0.65174,MA0154.1;2.6528,MA0155.1;1.01632,MA0156.1;0.0971366,MA0157.1;0.367703,MA0158.1;0,MA0159.1;0.450931,MA0160.1;1.13321,MA0161.1;0,MA0162.1;0.0159347,MA0163.1;0.818455,MA0164.1;1.51026,MA0080.2;0.0856322,MA0018.2;0.288301,MA0099.2;0.229319,MA0079.2;0.00354552,MA0102.2;1.07547,MA0258.1;1.93664,MA0259.1;0.214864,MA0442.1;0}}
|full_id=C481_lymph_vein_tonsil_appendix_submaxillary_trachea_temporal
|id=C481
}}

Latest revision as of 11:24, 17 September 2013


Full id: C481_lymph_vein_tonsil_appendix_submaxillary_trachea_temporal



Phase1 CAGE Peaks

Hg19::chr14:106208703..106208728,-p1@JN222933
p1@S76144
Hg19::chr14:106209113..106209156,+p@chr14:106209113..106209156
+
Hg19::chr14:106209338..106209364,+p@chr14:106209338..106209364
+
Hg19::chr14:106209368..106209399,-p1@IGHG1
Hg19::chr14:106236279..106236286,-p@chr14:106236279..106236286
-
Hg19::chr14:106237042..106237061,-p@chr14:106237042..106237061
-
Hg19::chr14:106321278..106321330,-p1@J00257
Hg19::chr14:106642049..106642054,-p1@IGHV1-18
Hg19::chr20:3687858..3687862,-p1@SIGLEC1
Hg19::chr22:22676808..22676813,+p1@IGLV1-51
Hg19::chr22:23237875..23237897,+p@chr22:23237875..23237897
+
Hg19::chr22:23237884..23237916,-p@chr22:23237884..23237916
-
Hg19::chr2:89156823..89156840,-p@chr2:89156823..89156840
-
Hg19::chr2:89156853..89156874,-p@chr2:89156853..89156874
-
Hg19::chr2:89157057..89157073,+p5@CU688247
p5@CU689025
p5@CU689831
p5@CU689833
p5@CU689835
p5@CU691143
Hg19::chr2:90007649..90007660,+p1@IGKV1D-27
Hg19::chr9:34691263..34691278,-p1@CCL19
Hg19::chr9:34709547..34709591,+p@chr9:34709547..34709591
+
Hg19::chr9:34709874..34709885,-p@chr9:34709874..34709885
-
Hg19::chr9:34710125..34710140,-p1@CCL21


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:0006954inflammatory response0.000145883258857863
GO:0009611response to wounding0.000224102063886895
GO:0006952defense response0.000298296102949237
GO:0009605response to external stimulus0.000298296102949237
GO:0008009chemokine activity0.000298296102949237
GO:0042379chemokine receptor binding0.000298296102949237
GO:0001664G-protein-coupled receptor binding0.000467526340171569
GO:0042330taxis0.000697921044060905
GO:0006935chemotaxis0.000697921044060905
GO:0006955immune response0.000888594413708518
GO:0007626locomotory behavior0.000888594413708518
GO:0006950response to stress0.000888594413708518
GO:0002376immune system process0.00119268236723501
GO:0007610behavior0.00186582398897099
GO:0005125cytokine activity0.00193525642725649
GO:0005615extracellular space0.00522505994912853
GO:0042221response to chemical stimulus0.0061060531140756
GO:0044421extracellular region part0.013598993597661
GO:0005515protein binding0.0153227288807027
GO:0005102receptor binding0.015815430263547
GO:0009615response to virus0.0309701819201496
GO:0007160cell-matrix adhesion0.0309701819201496
GO:0031589cell-substrate adhesion0.0309701819201496
GO:0006874cellular calcium ion homeostasis0.031476901111509
GO:0055074calcium ion homeostasis0.031476901111509
GO:0006875cellular metal ion homeostasis0.031476901111509
GO:0055065metal ion homeostasis0.031476901111509
GO:0003823antigen binding0.0420367370657912
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0420367370657912
GO:0055066di-, tri-valent inorganic cation homeostasis0.0420367370657912
GO:0030003cellular cation homeostasis0.0429745128846612
GO:0055080cation homeostasis0.0429745128846612
GO:0051707response to other organism0.0429745128846612
GO:0055082cellular chemical homeostasis0.0465524847824084
GO:0006873cellular ion homeostasis0.0465524847824084



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
B cell1.85e-2314
lymphocyte of B lineage2.25e-1824
pro-B cell2.25e-1824
lymphoid lineage restricted progenitor cell3.93e-0752
lymphocyte5.94e-0753
common lymphoid progenitor5.94e-0753
Uber Anatomy
Ontology termp-valuen
adult organism2.48e-37114
gland of gut8.02e-0910
major salivary gland1.03e-082
hemopoietic organ3.57e-087
immune organ3.57e-087
subdivision of digestive tract1.50e-07118
digestive system8.01e-07145
digestive tract8.01e-07145
primitive gut8.01e-07145


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)
MA0003.10.0152062
MA0004.10.180726
MA0006.10.597254
MA0007.10.502605
MA0009.10.561062
MA0014.10.0390946
MA0017.12.97266
MA0019.10.290278
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.0924235
MA0029.10.484339
MA0030.10.474212
MA0031.10.41796
MA0038.10.709504
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.10.561349
MA0046.10.551181
MA0048.10.418238
MA0050.10.512765
MA0051.10.251994
MA0052.10.492957
MA0055.11.94281
MA0056.10
MA0057.10.224163
MA0058.10.119655
MA0059.10.118893
MA0060.10.136253
MA0061.10.107862
MA0063.10
MA0066.13.70517
MA0067.10.858361
MA0068.10.0731654
MA0069.12.3178
MA0070.10.537571
MA0071.10.641904
MA0072.10.533514
MA0073.10.00109971
MA0074.10.251422
MA0076.10.129195
MA0077.10.526569
MA0078.10.33032
MA0081.10.37884
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.10.107101
MA0089.10
MA0090.11.36506
MA0091.10.537838
MA0092.10.925428
MA0093.10.0855877
MA0095.10
MA0098.10
MA0100.10.265855
MA0101.10.0872967
MA0103.10.970204
MA0105.10.0885831
MA0106.10.782788
MA0107.10.195292
MA0108.21.06707
MA0109.10
MA0111.10.146643
MA0113.10.300221
MA0114.13.98453
MA0115.11.84688
MA0116.12.77299
MA0117.10.595385
MA0119.10.718217
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.345226
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.0959198
MA0140.10.224213
MA0141.10.375925
MA0142.10.39079
MA0143.10.300362
MA0144.10.171577
MA0145.10.85225
MA0146.11.79544
MA0147.10.0556388
MA0148.10.198049
MA0149.10.21714
MA0062.20.0239298
MA0035.20.223695
MA0039.20.0406231
MA0138.20.882113
MA0002.20.123692
MA0137.20.0959012
MA0104.20.135419
MA0047.20.277681
MA0112.24.46229
MA0065.24.16035
MA0150.11.94158
MA0151.10
MA0152.10.648673
MA0153.10.65174
MA0154.12.6528
MA0155.11.01632
MA0156.10.0971366
MA0157.10.367703
MA0158.10
MA0159.10.450931
MA0160.11.13321
MA0161.10
MA0162.10.0159347
MA0163.10.818455
MA0164.11.51026
MA0080.20.0856322
MA0018.20.288301
MA0099.20.229319
MA0079.20.00354552
MA0102.21.07547
MA0258.11.93664
MA0259.10.214864
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

No analysis results for this cluster

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.

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