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Coexpression cluster:C1170: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.75236,0.384703,0.529489,0.343148,0.52784,0.604235,0.643217,0.224331,0.200685,0.497563,0.647852,0.184039,0.592674,0.905441,0.365029,0.827563,1.43406,0.19568,0.66776,0.384762,0.498384,0.520063,0.897212,0.430372,0.670692,0.164928,0.517892,0.346214,0.898182,0.475674,0.864517,0.257226,0.186138,0.309012,0.232776,0.825031,0.529001,0.282922,0.597792,0.829015,0.459366,0.254304,0.340293,0.494995,0.415364,0.60533,0.486696,0.237549,0.346342,0.684981,0.617179,0.752493,0.941629,1.09491,0.595623,0.350547,1.38261,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.88003,0.711163,1.65172,1.27705,1.01423,0.881388,2.06836,0.343884,0.759662,0.194299,2.13136,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,1.02467,0.915771,0.379203,0.507004,1.22894,0.304323,0.039977,0.474472,1.80003,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.854586,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,1.16378,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.0992692
|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;0.0156227,MA0017.1;0.991615,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;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;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.065183,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;1.67751,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;1.37625,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,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;1.36091,MA0115.1;1.21667,MA0116.1;0.760835,MA0117.1;1.01134,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;1.83545,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.276317,MA0146.1;0.0610556,MA0147.1;0.281049,MA0148.1;1.30922,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;2.60575,MA0112.2;0.262665,MA0065.2;1.48254,MA0150.1;0.430951,MA0151.1;0,MA0152.1;1.40145,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;1.89358,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.770207,MA0160.1;1.34201,MA0161.1;0,MA0162.1;0.0249953,MA0163.1;0.0765396,MA0164.1;1.62495,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;1.40221,MA0079.2;0.122495,MA0102.2;1.51913,MA0258.1;0.687127,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:45, 22 January 2013


Full id: C1170_Placental_Bronchial_nasal_Esophageal_Urothelial_Corneal_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr12:52880960..52880967,+p@chr12:52880960..52880967
+
Hg19::chr12:52887237..52887248,-p12@KRT6A
Hg19::chr12:52910884..52910895,-p5@S90014
Hg19::chr17:39775692..39775700,+p3@CU687211
Hg19::chr17:39775802..39775834,+p2@CU687211
Hg19::chr17:39775895..39775909,+p1@CU687211
Hg19::chr17:39777946..39777977,+p@chr17:39777946..39777977
+


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:0005200structural constituent of cytoskeleton0.0458495231367008
GO:0007398ectoderm development0.0458495231367008
GO:0008284positive regulation of cell proliferation0.0458495231367008
GO:0045111intermediate filament cytoskeleton0.0458495231367008
GO:0005882intermediate filament0.0458495231367008
GO:0009888tissue development0.0493789002708113



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 cell5.80e-29253
endo-epithelial cell6.64e-2942
respiratory epithelial cell3.72e-2213
endodermal cell3.83e-2158
general ecto-epithelial cell2.83e-2014
transitional epithelial cell4.97e-134
urothelial cell4.97e-134
epithelial cell of alimentary canal1.14e-1220
epithelial cell of tracheobronchial tree2.06e-129
epithelial cell of lower respiratory tract2.06e-129
ecto-epithelial cell1.74e-1034
bronchial epithelial cell2.22e-103
duct epithelial cell2.28e-103
branched duct epithelial cell2.28e-103
tracheal epithelial cell2.28e-103
tracheoblast2.28e-103
placental epithelial cell4.34e-103
epithelial cell of Malassez7.92e-103
gingival epithelial cell8.41e-103
acinar cell1.27e-095
extraembryonic cell1.15e-0819
stratified squamous epithelial cell1.38e-086
keratin accumulating cell1.38e-086
stratified epithelial cell1.38e-086
keratinizing barrier epithelial cell1.38e-086
epithelial fate stem cell1.38e-086
stratified epithelial stem cell1.38e-086
surface ectodermal cell1.38e-086
epidermal cell2.23e-089
protein secreting cell5.09e-086
corneal epithelial cell1.78e-072
mammary gland epithelial cell2.11e-074
sebum secreting cell6.19e-072
epithelial cell of sweat gland6.19e-072
epithelial cell of skin gland6.19e-072
acinar cell of sebaceous gland6.19e-072
squamous epithelial cell7.02e-0763
Uber Anatomy
Ontology termp-valuen
respiratory system2.13e-2174
endoderm-derived structure2.36e-21160
endoderm2.36e-21160
presumptive endoderm2.36e-21160
respiratory tract3.84e-1854
urothelium2.60e-155
segment of respiratory tract1.89e-1347
transitional epithelium1.07e-126
extraembryonic membrane2.91e-1214
membranous layer2.91e-1214
respiratory primordium8.33e-1238
endoderm of foregut8.33e-1238
surface structure6.57e-1199
digestive system7.56e-11145
digestive tract7.56e-11145
primitive gut7.56e-11145
larynx1.90e-109
lower respiratory tract epithelium2.22e-103
epithelium of bronchus2.22e-103
foregut2.81e-1087
upper respiratory tract5.69e-1019
gingival epithelium8.41e-103
organ part1.52e-09218
subdivision of digestive tract1.77e-09118
tracheobronchial tree2.71e-0915
lower respiratory tract2.71e-0915
oral opening7.22e-0922
orifice9.20e-0936
tongue1.40e-083
gustatory system1.40e-083
future tongue1.40e-083
head3.07e-0856
mouth6.20e-0829
stomodeum6.20e-0829
placenta1.19e-074
allantois1.19e-074
mouth mucosa1.53e-0713
jaw skeleton1.85e-074
splanchnocranium1.85e-074
mammary gland2.11e-074
mammary bud2.11e-074
mammary ridge2.11e-074
mammary placode2.11e-074
chorion2.94e-077
trachea3.52e-077
respiratory airway3.52e-077
anterior region of body4.03e-0762
craniocervical region4.03e-0762
thoracic cavity element5.58e-0734
thoracic cavity5.58e-0734
skin gland6.19e-072
epidermis gland6.19e-072
gland of integumental system6.19e-072
sebaceous gland6.19e-072
skin sebaceous gland6.19e-072
sweat gland6.19e-072
sweat gland placode6.19e-072
sebaceous gland placode6.19e-072
Disease
Ontology termp-valuen
squamous cell carcinoma1.27e-0814


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
MA0014.10.0156227
MA0017.10.991615
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
MA0042.10.48922
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
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.065183
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.11.67751
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.11.37625
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
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
MA0114.11.36091
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
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
MA0141.11.83545
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.0610556
MA0147.10.281049
MA0148.11.30922
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.22.60575
MA0112.20.262665
MA0065.21.48254
MA0150.10.430951
MA0151.10
MA0152.11.40145
MA0153.11.07307
MA0154.10.102476
MA0155.11.89358
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.11.34201
MA0161.10
MA0162.10.0249953
MA0163.10.0765396
MA0164.11.62495
MA0080.20.344472
MA0018.20.650405
MA0099.21.40221
MA0079.20.122495
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

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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