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Coexpression cluster:C379: Difference between revisions

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{{Coexpression_clusters
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79339,2.20938,0.088911,0.904059,2.13122,0.00555106,0.114422,0.697406,0.503302,0.115713,6.80815,2.08255,0.11321,0.27793,2.95526,0.0361212,0.00375807,0.840084,0.159157,0.313134,0.0895191,0.623045,0.210045,1.53488,0.597553,0.402924,0.532737,0.153325,0.991668,0.134204,8.27304,0.825331,0.373766,0.1606,0.750256,0.792735,0.171703,2.89679,0.611096,0.954146,0.33304,0.800453,0.261495,0.0114139,0.00104234,0.530988,0.083967,2.92366,5.90873,0.278987,0.330507,0.506215,0.0070601,0.290785,0.171482,0.0109843,0.486416,0.0704614,1.1244,0.81456,0.227861,1.04966,1.66156,0.463366,0.354445,0.0170841,0.340966,0.0197413,1.93766,0.388689,0.231068,0.039106,0.0213267,0.349965,0.384158,1.52905,0.25774,0.321489,0.303327,0.456614,0.24191,0.566144,0.0549789,0.381914,0.0488919,0.340192,0.652077,0.267503,0.0123006,1.53553,2.06923,0.0799445,0.523757,0.226179,0.113636,0.178598,0.753832,0.27955,0.154657,0.358416,0.561176,0.222109,0.463953,0.30248,0.573914,0.176484,0.707783,0.0135319,2.07861,0.720987,0.668879,1.49486,1.10037,0.634967,0.155698,0.385822,0.71827,0.129436,0.24704,1.33792,0.576539,3.20399,1.23954,0.000149682,0.464277,0.71028,0.160304,0.829202,1.16359,0.133083,0.242284,0.208636,0.633868,0.448609,0.329893,0.0584032,0.270734,0.170987,8.31898,0.157687,3.47893|tfbs_overrepresentation_jaspar=MA0003.1;0.541828,MA0004.1;0.102156,MA0006.1;0.0364375,MA0007.1;0.0928194,MA0009.1;8.72766,MA0014.1;2.94882,MA0017.1;1.57979,MA0019.1;0.188957,MA0024.1;0.9086,MA0025.1;0.544326,MA0027.1;1.97447,MA0028.1;0.367506,MA0029.1;0.942823,MA0030.1;0.349473,MA0031.1;0.299024,MA0038.1;0.160193,MA0040.1;0.363365,MA0041.1;0.360103,MA0042.1;0.0954223,MA0043.1;0.429296,MA0046.1;0.419892,MA0048.1;0.0304052,MA0050.1;0.0958601,MA0051.1;0.157595,MA0052.1;0.366488,MA0055.1;0.108027,MA0056.1;0,MA0057.1;2.03794,MA0058.1;0.810579,MA0059.1;5.70828,MA0060.1;0.0102756,MA0061.1;13.8967,MA0063.1;0,MA0066.1;0.938982,MA0067.1;0.711124,MA0068.1;0.451179,MA0069.1;0.416668,MA0070.1;1.04968,MA0071.1;0.137013,MA0072.1;0.403605,MA0073.1;3.08495,MA0074.1;0.157134,MA0076.1;0.065346,MA0077.1;0.397221,MA0078.1;0.222673,MA0081.1;0.0584929,MA0083.1;0.435361,MA0084.1;0.887042,MA0087.1;0.401577,MA0088.1;1.55672,MA0089.1;0,MA0090.1;0.533979,MA0091.1;0.103495,MA0092.1;0.0849313,MA0093.1;0.037369,MA0095.1;0,MA0098.1;0,MA0100.1;0.168841,MA0101.1;0.150934,MA0103.1;1.31244,MA0105.1;13.0468,MA0106.1;0.18641,MA0107.1;2.80804,MA0108.2;0.296685,MA0109.1;0,MA0111.1;1.42833,MA0113.1;0.197248,MA0114.1;0.207446,MA0115.1;0.640975,MA0116.1;3.40694,MA0117.1;0.460927,MA0119.1;0.754603,MA0122.1;0.483183,MA0124.1;0.60338,MA0125.1;0.528543,MA0130.1;0,MA0131.1;0.23543,MA0132.1;0,MA0133.1;0,MA0135.1;0.454747,MA0136.1;0.955971,MA0139.1;0.091521,MA0140.1;0.135474,MA0141.1;0.0577507,MA0142.1;0.275028,MA0143.1;0.197366,MA0144.1;0.015301,MA0145.1;0.129881,MA0146.1;2.05492,MA0147.1;0.433253,MA0148.1;0.115217,MA0149.1;14.0011,MA0062.2;0.861806,MA0035.2;3.35622,MA0039.2;0.447375,MA0138.2;0.223528,MA0002.2;0.124839,MA0137.2;0.0436553,MA0104.2;0.487307,MA0047.2;0.178535,MA0112.2;9.20052,MA0065.2;2.47286,MA0150.1;0.0689331,MA0151.1;0,MA0152.1;1.37237,MA0153.1;0.513757,MA0154.1;12.2012,MA0155.1;4.62736,MA0156.1;1.99958,MA0157.1;0.254856,MA0158.1;0,MA0159.1;6.78399,MA0160.1;0.123537,MA0161.1;0,MA0162.1;0.00023736,MA0163.1;0.153605,MA0164.1;1.12038,MA0080.2;1.38005,MA0018.2;0.187315,MA0099.2;0.431402,MA0079.2;16.2223,MA0102.2;0.922526,MA0258.1;2.498,MA0259.1;0.241418,MA0442.1;0}}
|full_id=C379_Preadipocyte_Adipocyte_tenocyte_Chondrocyte_basal_aorta_trachea
|id=C379
|ontology_enrichment_celltype=CL:0000055!5.19e-16!180;CL:0000057!7.01e-11!75;CL:0000136!4.22e-09!15
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.41e-23!115;UBERON:0000475!6.81e-17!365;UBERON:0000073!1.18e-16!94;UBERON:0001016!1.18e-16!94;UBERON:0005743!3.23e-16!86;UBERON:0001017!1.78e-14!82;UBERON:0001049!6.68e-14!57;UBERON:0005068!6.68e-14!57;UBERON:0006241!6.68e-14!57;UBERON:0007135!6.68e-14!57;UBERON:0000924!1.32e-13!173;UBERON:0006601!1.32e-13!173;UBERON:0002346!2.51e-13!90;UBERON:0004121!4.79e-13!169;UBERON:0003075!8.76e-13!86;UBERON:0007284!8.76e-13!86;UBERON:0002616!9.34e-13!59;UBERON:0000955!2.38e-11!69;UBERON:0006238!2.38e-11!69;UBERON:0000153!2.51e-11!129;UBERON:0007811!2.51e-11!129;UBERON:0000033!6.09e-11!123;UBERON:0003080!2.32e-09!42;UBERON:0002780!5.54e-09!41;UBERON:0001890!5.54e-09!41;UBERON:0006240!5.54e-09!41;UBERON:0000468!2.70e-08!659;UBERON:0003056!5.74e-08!61;UBERON:0000481!7.57e-08!347;UBERON:0001893!1.01e-07!34;UBERON:0002020!1.06e-07!34;UBERON:0003528!1.06e-07!34;UBERON:0002791!1.29e-07!33;UBERON:0001869!3.35e-07!32
}}

Latest revision as of 11:21, 17 September 2013


Full id: C379_Preadipocyte_Adipocyte_tenocyte_Chondrocyte_basal_aorta_trachea



Phase1 CAGE Peaks

Hg19::chr7:73442422..73442447,+p2@ELN
Hg19::chr7:73442457..73442475,+p3@ELN
Hg19::chr7:73442494..73442517,+p1@ELN
Hg19::chr7:73469042..73469059,+p@chr7:73469042..73469059
+
Hg19::chr7:73470651..73470669,+p@chr7:73470651..73470669
+
Hg19::chr7:73477638..73477666,+p@chr7:73477638..73477666
+
Hg19::chr7:73477950..73477995,+p@chr7:73477950..73477995
+
Hg19::chr7:73480017..73480028,+p@chr7:73480017..73480028
+
Hg19::chr7:73482988..73482997,+p24@ELN
Hg19::chr7:73483140..73483149,+p31@ELN
Hg19::chr7:73483243..73483250,+p32@ELN
Hg19::chr7:73483251..73483276,+p12@ELN
Hg19::chr7:73483317..73483330,+p15@ELN
Hg19::chr7:73483322..73483337,-p@chr7:73483322..73483337
-
Hg19::chr7:73483368..73483378,+p21@ELN
Hg19::chr7:73483383..73483410,+p4@ELN
Hg19::chr7:73483422..73483429,+p27@ELN
Hg19::chr7:73483434..73483454,+p5@ELN
Hg19::chr7:73483509..73483536,+p10@ELN
Hg19::chr7:73483549..73483572,+p6@ELN
Hg19::chr7:73483600..73483621,+p13@ELN
Hg19::chr7:73483627..73483640,+p11@ELN
Hg19::chr7:73483650..73483661,+p22@ELN
Hg19::chr7:73483658..73483686,-p@chr7:73483658..73483686
-
Hg19::chr7:73483727..73483738,-p@chr7:73483727..73483738
-
Hg19::chr7:73483740..73483747,+p26@ELN
Hg19::chr7:73483843..73483855,+p23@ELN
Hg19::chr7:73483852..73483863,-p@chr7:73483852..73483863
-
Hg19::chr7:73483886..73483914,-p@chr7:73483886..73483914
-


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

No GOStat results

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
fibroblast1.83e-1476
skin fibroblast3.09e-1223
fat cell1.62e-0915
preadipocyte6.82e-0812
GAG secreting cell1.34e-079
carbohydrate secreting cell1.34e-079
adipocyte of omentum tissue1.66e-073
preadipocyte of the breast2.21e-073
omentum preadipocyte5.51e-073
fibrocyte5.96e-073
attachment cell5.96e-073
tendon cell5.96e-073
Uber Anatomy
Ontology termp-valuen
omentum7.87e-136
peritoneum7.87e-136
abdominal cavity7.87e-136
visceral peritoneum7.87e-136
cavity lining8.23e-1312
serous membrane8.23e-1312
skin of body9.20e-0941
integument2.34e-0846
integumental system2.34e-0846
dense regular connective tissue5.96e-073
tendon5.96e-073
regular connective tissue5.96e-073


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)
MA0003.10.541828
MA0004.10.102156
MA0006.10.0364375
MA0007.10.0928194
MA0009.18.72766
MA0014.12.94882
MA0017.11.57979
MA0019.10.188957
MA0024.10.9086
MA0025.10.544326
MA0027.11.97447
MA0028.10.367506
MA0029.10.942823
MA0030.10.349473
MA0031.10.299024
MA0038.10.160193
MA0040.10.363365
MA0041.10.360103
MA0042.10.0954223
MA0043.10.429296
MA0046.10.419892
MA0048.10.0304052
MA0050.10.0958601
MA0051.10.157595
MA0052.10.366488
MA0055.10.108027
MA0056.10
MA0057.12.03794
MA0058.10.810579
MA0059.15.70828
MA0060.10.0102756
MA0061.113.8967
MA0063.10
MA0066.10.938982
MA0067.10.711124
MA0068.10.451179
MA0069.10.416668
MA0070.11.04968
MA0071.10.137013
MA0072.10.403605
MA0073.13.08495
MA0074.10.157134
MA0076.10.065346
MA0077.10.397221
MA0078.10.222673
MA0081.10.0584929
MA0083.10.435361
MA0084.10.887042
MA0087.10.401577
MA0088.11.55672
MA0089.10
MA0090.10.533979
MA0091.10.103495
MA0092.10.0849313
MA0093.10.037369
MA0095.10
MA0098.10
MA0100.10.168841
MA0101.10.150934
MA0103.11.31244
MA0105.113.0468
MA0106.10.18641
MA0107.12.80804
MA0108.20.296685
MA0109.10
MA0111.11.42833
MA0113.10.197248
MA0114.10.207446
MA0115.10.640975
MA0116.13.40694
MA0117.10.460927
MA0119.10.754603
MA0122.10.483183
MA0124.10.60338
MA0125.10.528543
MA0130.10
MA0131.10.23543
MA0132.10
MA0133.10
MA0135.10.454747
MA0136.10.955971
MA0139.10.091521
MA0140.10.135474
MA0141.10.0577507
MA0142.10.275028
MA0143.10.197366
MA0144.10.015301
MA0145.10.129881
MA0146.12.05492
MA0147.10.433253
MA0148.10.115217
MA0149.114.0011
MA0062.20.861806
MA0035.23.35622
MA0039.20.447375
MA0138.20.223528
MA0002.20.124839
MA0137.20.0436553
MA0104.20.487307
MA0047.20.178535
MA0112.29.20052
MA0065.22.47286
MA0150.10.0689331
MA0151.10
MA0152.11.37237
MA0153.10.513757
MA0154.112.2012
MA0155.14.62736
MA0156.11.99958
MA0157.10.254856
MA0158.10
MA0159.16.78399
MA0160.10.123537
MA0161.10
MA0162.10.00023736
MA0163.10.153605
MA0164.11.12038
MA0080.21.38005
MA0018.20.187315
MA0099.20.431402
MA0079.216.2223
MA0102.20.922526
MA0258.12.498
MA0259.10.241418
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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