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Coexpression cluster:C1155: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.01633,0.465735,1.00019,0.529489,0.343148,0.52784,0.604235,0.226729,0.637583,0.443077,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.28906,0.569568,0.66776,0.384762,0.0646572,0.520063,0.338096,0.430372,0.670692,0.164928,0.517892,0.346214,0.459534,0.475674,0.864517,0.257226,1.64836,0.309012,0.442372,0.305874,0.529001,0.282922,0.207499,0.829015,0.459366,0.0729319,1.61728,1.57451,0.415364,1.47235,0.486696,0.0670664,0.346342,0.684981,0.617179,1.79619,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.656075,0.115253,1.0929,0.531388,0.503161,0.473656,0.782748,0.850825,1.0864,1.099,0.798651,0.625403,1.21234,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.566252,0.924148,0.715799,1.32948,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.155979,0.474472,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.854586,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,2.99223,0.26104,1.16062,0.241704,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.033943
|tfbs_overrepresentation_jaspar=MA0003.1;0.110456,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.187674,MA0017.1;2.64218,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;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;1.22641,MA0043.1;0.973609,MA0046.1;2.20916,MA0048.1;0.382278,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.0407081,MA0056.1;0,MA0057.1;0.369442,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;1.09187,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.488375,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.0282921,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.0723293,MA0089.1;0,MA0090.1;1.95014,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.918548,MA0103.1;2.40787,MA0105.1;1.14871,MA0106.1;1.56379,MA0107.1;0.752965,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;3.81523,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;2.30913,MA0119.1;0.388712,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;1.04059,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;1.30855,MA0145.1;0.276317,MA0146.1;0.324987,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.60756,MA0138.2;0.704862,MA0002.2;0.611548,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;1.53797,MA0112.2;1.41281,MA0065.2;4.05005,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;2.43458,MA0154.1;0.102476,MA0155.1;0.910701,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.770207,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.0249953,MA0163.1;0.0167306,MA0164.1;1.62495,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;1.40221,MA0079.2;0.361922,MA0102.2;1.51913,MA0258.1;0.687127,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:44, 22 January 2013


Full id: C1155_Hepatocyte_Intestinal_Prostate_liver_colon_small_Retinal



Phase1 CAGE Peaks

Hg19::chr11:74870848..74870885,+p3@SLCO2B1
Hg19::chr11:74870889..74870902,+p5@SLCO2B1
Hg19::chr11:74870904..74870913,+p10@SLCO2B1
Hg19::chr1:209827344..209827383,-p@chr1:209827344..209827383
-
Hg19::chr22:50738736..50738785,-p@chr22:50738736..50738785
-
Hg19::chr6:126221034..126221056,+p13@NCOA7
Hg19::chr6:170190148..170190182,+p1@C6orf208


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:0016998cell wall catabolic process0.0139189274041004
GO:0010382cell wall metabolic process0.0139189274041004
GO:0007047cell wall organization and biogenesis0.0139189274041004
GO:0045229external encapsulating structure organization and biogenesis0.0139189274041004



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
metabolising cell1.24e-2112
endopolyploid cell1.24e-2112
parenchymal cell1.24e-2112
polyploid cell1.24e-2112
hepatocyte1.24e-2112
endodermal cell2.64e-1158
intestinal epithelial cell9.27e-074
Uber Anatomy
Ontology termp-valuen
intestine4.28e-2917
gastrointestinal system5.92e-2825
sac1.71e-2326
digestive tract diverticulum3.06e-2223
liver3.67e-2219
digestive gland3.67e-2219
liver bud3.67e-2219
epithelial sac2.99e-2025
epithelium of foregut-midgut junction3.19e-2025
anatomical boundary3.19e-2025
hepatobiliary system3.19e-2025
foregut-midgut junction3.19e-2025
septum transversum3.19e-2025
subdivision of digestive tract1.78e-19118
hepatic diverticulum6.24e-1922
liver primordium6.24e-1922
large intestine1.67e-1711
abdomen element8.57e-1754
abdominal segment element8.57e-1754
digestive system1.72e-16145
digestive tract1.72e-16145
primitive gut1.72e-16145
colon2.92e-159
abdominal segment of trunk8.02e-1560
abdomen8.02e-1560
gut epithelium9.31e-1554
endoderm-derived structure1.80e-14160
endoderm1.80e-14160
presumptive endoderm1.80e-14160
exocrine gland5.46e-1331
exocrine system5.46e-1331
endocrine gland2.50e-1135
organ system subdivision8.38e-11223
small intestine9.94e-114
lower digestive tract1.68e-105
endo-epithelium2.58e-1082
trunk region element6.53e-09101
endocrine system1.78e-0845
multi-tissue structure3.33e-08342
subdivision of trunk9.68e-08112
gland1.23e-0759
anatomical cluster6.00e-07373
intestinal mucosa9.27e-074
wall of intestine9.27e-074
gastrointestinal system mucosa9.27e-074
gastrointestinal system epithelium9.27e-074
intestinal epithelium9.27e-074
vermiform appendix9.79e-071
caecum9.79e-071
midgut9.79e-071


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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.12.64218
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.11.22641
MA0043.10.973609
MA0046.12.20916
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.11.09187
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0282921
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.11.95014
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.12.40787
MA0105.11.14871
MA0106.11.56379
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.13.81523
MA0115.11.21667
MA0116.10.277571
MA0117.12.30913
MA0119.10.388712
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
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.11.30855
MA0145.10.276317
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.60756
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.21.53797
MA0112.21.41281
MA0065.24.05005
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.12.43458
MA0154.10.102476
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.11.62495
MA0080.20.344472
MA0018.20.650405
MA0099.21.40221
MA0079.20.361922
MA0102.21.51913
MA0258.10.687127
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
EP300#203354.838529804445140.001132708190785470.00775628840397612
FOXA2#3170414.07455071580878.60810644096383e-050.00128966006109284
HDAC2#306635.749551529982680.01153041704040530.0421721318607211
HEY1#2346252.885793602218360.01231366941853030.0446258352558083
HNF4A#3172516.52306454496692.94289296346546e-060.000100870626259064
HNF4G#3174520.5381589474621.00601446599988e-064.25028902971529e-05
TCF7L2#693446.154386607507050.002064676148138040.0119702849025973



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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