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Coexpression cluster:C484: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.111472,1.58615,0.107302,0.19904,0.287896,0.574869,0.253108,0.324098,0.31878,0.13723,1.00751,0.780773,0.0213511,0.684702,0.285984,0.319274,0.43322,0.468601,0.105136,0.176245,4.51552,3.1056,0.192508,0.280777,0.827313,0.304148,1.29742,0.558352,0.0865304,0.559665,0.489389,0.465029,0.0458359,0.449456,0.517019,0.117893,0.0667305,0.1987,0.206488,0.117466,0.0675531,0.152186,1.68118,0.0834931,0.24565,0.125045,1.30473,1.55564,2.31673,0.609855,0.315441,0.262847,0.229319,0.532773,0.671855,0.246686,0.0887806,0.222594,0.332598,0.631782,1.25147,0.255713,0.319823,0.409576,0.269358,0.380605,0.754286,1.10771,0.456006,0.950487,0.143869,0.336341,0.00682481,0.670004,0.020227,0.390082,3.63084,0.395294,2.00494,0.811071,0.266362,0.408665,0.269087,0.141606,0.622646,0.0608845,0.0781398,0.539405,0.336397,1.20481,0.84263,1.45696,0.4797,0.0486298,0.0853298,0.768543,0.477063,0.517267,0.340143,0.473931,0.208183,0.474756,0.512318,0.436368,1.72469,0.174162,0.422802,0.241933,0.417285,0.0770225,0.113655,0.509866,0.104228,0.183573,5.94126,0.505559,0.0136165,0.161925,0.378653,0.186375,0.662347,0.889041,0.195973,0.277756,0.90249,0.395934,0.248345,0.484077,0.701879,0.200186,0.598629,1.52431,0.715286,0.275188,0.854902,0.77879,0.932181,0.191402,0.814541,1.65405,1.25623,0.779227,0.249639,0.514137,0.372477,0.216494,0.35869,1.49614,0.457994,0.710803,1.84981,0.00178079,0.598976,0.127482,0.255347,0.980005,0.32333,0.960217,0.827468,0.116987,0.77808,0.582159,1.14758,0.118854,0.385896,0.268483,1.96581,2.80358,0.478654
|tfbs_overrepresentation_for_novel_motifs=0.111472,1.58615,0.107302,0.19904,0.287896,0.574869,0.253108,0.324098,0.31878,0.13723,1.00751,0.780773,0.0213511,0.684702,0.285984,0.319274,0.43322,0.468601,0.105136,0.176245,4.51552,3.1056,0.192508,0.280777,0.827313,0.304148,1.29742,0.558352,0.0865304,0.559665,0.489389,0.465029,0.0458359,0.449456,0.517019,0.117893,0.0667305,0.1987,0.206488,0.117466,0.0675531,0.152186,1.68118,0.0834931,0.24565,0.125045,1.30473,1.55564,2.31673,0.609855,0.315441,0.262847,0.229319,0.532773,0.671855,0.246686,0.0887806,0.222594,0.332598,0.631782,1.25147,0.255713,0.319823,0.409576,0.269358,0.380605,0.754286,1.10771,0.456006,0.950487,0.143869,0.336341,0.00682481,0.670004,0.020227,0.390082,3.63084,0.395294,2.00494,0.811071,0.266362,0.408665,0.269087,0.141606,0.622646,0.0608845,0.0781398,0.539405,0.336397,1.20481,0.84263,1.45696,0.4797,0.0486298,0.0853298,0.768543,0.477063,0.517267,0.340143,0.473931,0.208183,0.474756,0.512318,0.436368,1.72469,0.174162,0.422802,0.241933,0.417285,0.0770225,0.113655,0.509866,0.104228,0.183573,5.94126,0.505559,0.0136165,0.161925,0.378653,0.186375,0.662347,0.889041,0.195973,0.277756,0.90249,0.395934,0.248345,0.484077,0.701879,0.200186,0.598629,1.52431,0.715286,0.275188,0.854902,0.77879,0.932181,0.191402,0.814541,1.65405,1.25623,0.779227,0.249639,0.514137,0.372477,0.216494,0.35869,1.49614,0.457994,0.710803,1.84981,0.00178079,0.598976,0.127482,0.255347,0.980005,0.32333,0.960217,0.827468,0.116987,0.77808,0.582159,1.14758,0.118854,0.385896,0.268483,1.96581,2.80358,0.478654
|tfbs_overrepresentation_jaspar=MA0003.1;0.00108478,MA0004.1;0.180726,MA0006.1;0.0840255,MA0007.1;0.502605,MA0009.1;0.561062,MA0014.1;0.0390946,MA0017.1;0.697761,MA0019.1;0.789756,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;0.511308,MA0043.1;0.561349,MA0046.1;0.551181,MA0048.1;0.238801,MA0050.1;0.172223,MA0051.1;0.251994,MA0052.1;1.23441,MA0055.1;1.94281,MA0056.1;0,MA0057.1;1.57749,MA0058.1;0.380569,MA0059.1;0.378591,MA0060.1;0.0338613,MA0061.1;0.490814,MA0063.1;0,MA0066.1;1.31072,MA0067.1;0.858361,MA0068.1;0.370416,MA0069.1;0.547689,MA0070.1;0.537571,MA0071.1;0.22617,MA0072.1;0.533514,MA0073.1;0.0303421,MA0074.1;1.29537,MA0076.1;0.129195,MA0077.1;0.526569,MA0078.1;0.33032,MA0081.1;0.118989,MA0083.1;0.567893,MA0084.1;1.03923,MA0087.1;0.531309,MA0088.1;0.350415,MA0089.1;0,MA0090.1;1.36506,MA0091.1;0.182521,MA0092.1;0.475738,MA0093.1;0.289647,MA0095.1;0,MA0098.1;0,MA0100.1;0.265855,MA0101.1;1.02838,MA0103.1;0.27232,MA0105.1;0.0885831,MA0106.1;0.28721,MA0107.1;0.432984,MA0108.2;0.415325,MA0109.1;0,MA0111.1;0.449411,MA0113.1;1.47447,MA0114.1;0.739706,MA0115.1;0.785493,MA0116.1;0.199654,MA0117.1;0.595385,MA0119.1;0.109564,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;0.450711,MA0140.1;1.85803,MA0141.1;0.117869,MA0142.1;0.39079,MA0143.1;0.300362,MA0144.1;0.171577,MA0145.1;0.128234,MA0146.1;6.00758,MA0147.1;0.204087,MA0148.1;0.198049,MA0149.1;0.21714,MA0062.2;0.0239298,MA0035.2;1.19041,MA0039.2;0.0690952,MA0138.2;0.882113,MA0002.2;0.294582,MA0137.2;0.0959012,MA0104.2;0.0336072,MA0047.2;0.761085,MA0112.2;1.07495,MA0065.2;1.16658,MA0150.1;0.134443,MA0151.1;0,MA0152.1;0.229055,MA0153.1;0.65174,MA0154.1;2.6528,MA0155.1;1.31756,MA0156.1;0.0971366,MA0157.1;0.367703,MA0158.1;0,MA0159.1;0.204897,MA0160.1;0.601097,MA0161.1;0,MA0162.1;0.00498168,MA0163.1;0.337437,MA0164.1;0.310173,MA0080.2;0.0856322,MA0018.2;1.4313,MA0099.2;0.229319,MA0079.2;0.45214,MA0102.2;1.07547,MA0258.1;0.0413436,MA0259.1;0.0592752,MA0442.1;0
}}
}}

Revision as of 19:12, 22 January 2013


Full id: C484_squamous_pharyngeal_bile_transitionalcell_Prostate_signet_trachea



Phase1 CAGE Peaks

Hg19::chr9:130911723..130911741,+p1@LCN2
Hg19::chr9:130911770..130911779,+p2@LCN2
Hg19::chr9:130911904..130911915,-p@chr9:130911904..130911915
-
Hg19::chr9:130912519..130912545,+p@chr9:130912519..130912545
+
Hg19::chr9:130912567..130912578,-p@chr9:130912567..130912578
-
Hg19::chr9:130912602..130912627,+p@chr9:130912602..130912627
+
Hg19::chr9:130912603..130912639,-p@chr9:130912603..130912639
-
Hg19::chr9:130912628..130912633,+p@chr9:130912628..130912633
+
Hg19::chr9:130913926..130913932,+p4@LCN2
Hg19::chr9:130913939..130913973,+p3@LCN2
Hg19::chr9:130913945..130913957,-p@chr9:130913945..130913957
-
Hg19::chr9:130914190..130914206,+p@chr9:130914190..130914206
+
Hg19::chr9:130914212..130914239,+p@chr9:130914212..130914239
+
Hg19::chr9:130914227..130914253,-p@chr9:130914227..130914253
-
Hg19::chr9:130914276..130914284,+p@chr9:130914276..130914284
+
Hg19::chr9:130914283..130914293,-p@chr9:130914283..130914293
-
Hg19::chr9:130914494..130914509,+p@chr9:130914494..130914509
+
Hg19::chr9:130914521..130914530,+p@chr9:130914521..130914530
+
Hg19::chr9:130915632..130915647,+p@chr9:130915632..130915647
+
Hg19::chr9:130915665..130915685,-p@chr9:130915665..130915685
-


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell8.64e-14253
endo-epithelial cell3.01e-1342
endodermal cell2.41e-1058
epithelial cell of gall bladder6.09e-092
Uber Anatomy
Ontology termp-valuen
tongue2.02e-123
gustatory system2.02e-123
future tongue2.02e-123
endoderm-derived structure2.99e-12160
endoderm2.99e-12160
presumptive endoderm2.99e-12160
biliary system8.01e-119
biliary tree8.01e-119
biliary bud8.01e-119
digestive system1.15e-10145
digestive tract1.15e-10145
primitive gut1.15e-10145
subdivision of digestive tract1.41e-10118
orifice4.81e-0936
pharynx6.47e-0911
foregut6.76e-0987
throat1.02e-082
reproductive structure2.63e-0859
reproductive system2.63e-0859
respiratory tract9.41e-0854
respiratory system4.09e-0774
female reproductive organ5.19e-0737
female reproductive system5.19e-0737
Disease
Ontology termp-valuen
carcinoma2.77e-24106
squamous cell carcinoma5.75e-2114
adenocarcinoma2.99e-1725
cell type cancer3.58e-16143
signet ring cell adenocarcinoma5.85e-092
tubular adenocarcinoma6.59e-092
cancer6.71e-08235
disease of cellular proliferation1.34e-07239


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)
MA0003.10.00108478
MA0004.10.180726
MA0006.10.0840255
MA0007.10.502605
MA0009.10.561062
MA0014.10.0390946
MA0017.10.697761
MA0019.10.789756
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
MA0042.10.511308
MA0043.10.561349
MA0046.10.551181
MA0048.10.238801
MA0050.10.172223
MA0051.10.251994
MA0052.11.23441
MA0055.11.94281
MA0056.10
MA0057.11.57749
MA0058.10.380569
MA0059.10.378591
MA0060.10.0338613
MA0061.10.490814
MA0063.10
MA0066.11.31072
MA0067.10.858361
MA0068.10.370416
MA0069.10.547689
MA0070.10.537571
MA0071.10.22617
MA0072.10.533514
MA0073.10.0303421
MA0074.11.29537
MA0076.10.129195
MA0077.10.526569
MA0078.10.33032
MA0081.10.118989
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.10.350415
MA0089.10
MA0090.11.36506
MA0091.10.182521
MA0092.10.475738
MA0093.10.289647
MA0095.10
MA0098.10
MA0100.10.265855
MA0101.11.02838
MA0103.10.27232
MA0105.10.0885831
MA0106.10.28721
MA0107.10.432984
MA0108.20.415325
MA0109.10
MA0111.10.449411
MA0113.11.47447
MA0114.10.739706
MA0115.10.785493
MA0116.10.199654
MA0117.10.595385
MA0119.10.109564
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.345226
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.450711
MA0140.11.85803
MA0141.10.117869
MA0142.10.39079
MA0143.10.300362
MA0144.10.171577
MA0145.10.128234
MA0146.16.00758
MA0147.10.204087
MA0148.10.198049
MA0149.10.21714
MA0062.20.0239298
MA0035.21.19041
MA0039.20.0690952
MA0138.20.882113
MA0002.20.294582
MA0137.20.0959012
MA0104.20.0336072
MA0047.20.761085
MA0112.21.07495
MA0065.21.16658
MA0150.10.134443
MA0151.10
MA0152.10.229055
MA0153.10.65174
MA0154.12.6528
MA0155.11.31756
MA0156.10.0971366
MA0157.10.367703
MA0158.10
MA0159.10.204897
MA0160.10.601097
MA0161.10
MA0162.10.00498168
MA0163.10.337437
MA0164.10.310173
MA0080.20.0856322
MA0018.21.4313
MA0099.20.229319
MA0079.20.45214
MA0102.21.07547
MA0258.10.0413436
MA0259.10.0592752
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
GATA1#262353.390077035950110.01323321252295330.0468178686546316
TAL1#688657.467154169360050.000427161752698430.00399072781913153



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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