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Coexpression cluster:C1277: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.0232809,0.384703,0.529489,0.343148,0.52784,0.604235,0.643217,0.637583,2.19177,0.497563,0.647852,0.541517,6.148,0.341795,0.365029,0.827563,0.28906,1.08139,0.66776,0.384762,0.498384,0.520063,0.338096,0.430372,0.670692,0.164928,0.517892,0.346214,0.898182,0.475674,0.864517,1.31702,1.04347,0.309012,0.021349,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,1.91266,0.340293,0.109128,0.415364,0.60533,0.486696,0.511111,0.915545,1.63878,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,1.38261,0.150585,2.36353,0.905643,1.47735,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,2.94441,0.921933,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.310394,0.097572,0.146388,0.711163,1.65172,1.27705,2.315,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,3.29043,0.395884,0.915771,0.379203,0.507004,1.22894,1.48924,1.00084,5.34151,0.762789,1.35329,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,2.31423,0.241704,1.0153,0.216774,1.47633,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,1.84123,0.7715,0.624608,0.24928,0.602897,0.212606
|tfbs_overrepresentation_for_novel_motifs=0.392069,0.0232809,0.384703,0.529489,0.343148,0.52784,0.604235,0.643217,0.637583,2.19177,0.497563,0.647852,0.541517,6.148,0.341795,0.365029,0.827563,0.28906,1.08139,0.66776,0.384762,0.498384,0.520063,0.338096,0.430372,0.670692,0.164928,0.517892,0.346214,0.898182,0.475674,0.864517,1.31702,1.04347,0.309012,0.021349,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,1.91266,0.340293,0.109128,0.415364,0.60533,0.486696,0.511111,0.915545,1.63878,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,1.38261,0.150585,2.36353,0.905643,1.47735,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,2.94441,0.921933,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.310394,0.097572,0.146388,0.711163,1.65172,1.27705,2.315,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,3.29043,0.395884,0.915771,0.379203,0.507004,1.22894,1.48924,1.00084,5.34151,0.762789,1.35329,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,2.31423,0.241704,1.0153,0.216774,1.47633,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,1.84123,0.7715,0.624608,0.24928,0.602897,0.212606
|tfbs_overrepresentation_jaspar=MA0003.1;0.0462779,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0723474,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;1.47594,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.120314,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.0407081,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;2.16244,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.000265001,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;1.84202,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.538456,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;2.05178,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;4.77881,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;3.66623,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.547495,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.980834,MA0146.1;0.0610556,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.00276064,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.996317,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.071478,MA0156.1;2.57306,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.106355,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.000432051,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:49, 22 January 2013


Full id: C1277_Hepatocyte_mature_mesenchymal_smooth_bladder_normal_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr5:52083909..52083927,+p7@PELO
Hg19::chr5:52083929..52083940,+p12@PELO
Hg19::chr5:52083991..52084021,+p3@ITGA1
Hg19::chr5:52084023..52084051,+p2@ITGA1
Hg19::chr5:52084059..52084086,+p4@ITGA1
Hg19::chr5:52084087..52084115,+p5@ITGA1
Hg19::chr5:52084126..52084133,+p8@ITGA1


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:0045123cellular extravasation0.0155415249616414
GO:0030593neutrophil chemotaxis0.0223346942055352
GO:0005518collagen binding0.0223346942055352
GO:0030595leukocyte chemotaxis0.0223346942055352
GO:0050900leukocyte migration0.0240797902081608
GO:0009897external side of plasma membrane0.0305050789062747
GO:0008305integrin complex0.0305050789062747
GO:0007229integrin-mediated signaling pathway0.038793191786861
GO:0007160cell-matrix adhesion0.038793191786861
GO:0031589cell-substrate adhesion0.038793191786861
GO:0043235receptor complex0.038793191786861
GO:0042330taxis0.0409869718598991
GO:0006935chemotaxis0.0409869718598991
GO:0009986cell surface0.0409869718598991
GO:0007626locomotory behavior0.0467614554761341



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.49e-13114
multi-tissue structure4.99e-12342
anatomical cluster8.30e-11373
multi-cellular organism6.27e-10656
digestive system8.25e-10145
digestive tract8.25e-10145
primitive gut8.25e-10145
subdivision of digestive tract9.24e-10118
mesenchyme3.32e-08160
entire embryonic mesenchyme3.32e-08160
endoderm-derived structure4.05e-08160
endoderm4.05e-08160
presumptive endoderm4.05e-08160
primordium7.46e-08160
liver1.69e-0719
digestive gland1.69e-0719
liver bud1.69e-0719
trunk mesenchyme2.39e-07122
organ system subdivision2.81e-07223
sac4.22e-0726
trunk6.55e-07199
digestive tract diverticulum6.73e-0723
endocrine gland7.92e-0735
anatomical system9.39e-07624


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)
MA0003.10.0462779
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.11.47594
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.12.16244
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.84202
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.12.05178
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.14.77881
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.13.66623
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.980834
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.996317
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.12.57306
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.000432051
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
CEBPB#105177.971147625824824.88663622402061e-072.30200902390838e-05
CTCF#1066475.360256373075037.86114662284756e-060.00022249601413105
E2F1#186974.907389214879321.45832274679793e-050.000347017018347754
E2F6#187675.017155731697391.24910426162553e-050.000308331836397799
EP300#203376.77394172622321.52695018318475e-065.86729765201002e-05
FOXA2#3170724.63046375266521.81353313360781e-101.89214372568298e-08
HNF4A#3172723.13229036295372.81434373816722e-102.86199849727796e-08
HNF4G#3174728.75342252644686.13483972627905e-116.8379565226559e-09
POLR2A#543072.147453176558070.004747636447610280.0223582271250381
RAD21#588557.39645278246880.0001491014505228370.00192341976175328
SMARCB1#6598718.25271578115741.4786181847889e-091.31425876256313e-07
SMC3#9126510.74638060352352.42943476743625e-050.000527171696813369
SP1#666775.69838137814095.12280185510121e-060.000157358912630857
SRF#6722713.79717826216781.04914736064956e-087.9113286064173e-07
TAF1#687273.343046285745290.0002142336319622450.00246848480676356
TFAP2C#7022710.80922860986025.79365976833206e-083.61459995546495e-06
YY1#752874.911170749853861.45048003565243e-050.000345623281869732
ZNF263#1012778.221841637010683.93423095812578e-071.91021453759041e-05



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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