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Coexpression cluster:C1399: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,1.35536,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,1.30166,0.436569,0.6169,0.576478,0.387783,0.483957,0.730467,1.73917,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,0.640661,0.35719,0.134746,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,1.6253,0.390088,1.89526,0.468392,0.66382,0.542147,0.630853,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,1.03549,0.62023,2.34444,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,2.11566,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.562953,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.794988,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,1.91313,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,2.2605,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.8388,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,1.75096,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.152397
|tfbs_overrepresentation_jaspar=MA0003.1;0.321379,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;3.85762,MA0014.1;0.0254709,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;3.61901,MA0055.1;0.465994,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;1.24837,MA0063.1;0,MA0066.1;2.69973,MA0067.1;1.35893,MA0068.1;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.0214749,MA0074.1;1.58758,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;1.29635,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;1.81721,MA0103.1;1.76074,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;1.54633,MA0108.2;2.01717,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.845337,MA0115.1;1.28169,MA0116.1;2.36812,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;1.84113,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;0.093337,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.569061,MA0138.2;0.765223,MA0002.2;0.709311,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;3.64053,MA0065.2;1.18263,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;3.32265,MA0155.1;1.09123,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;1.46233,MA0161.1;0,MA0162.1;0.150673,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.476723,MA0102.2;1.58513,MA0258.1;3.98052,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 19:54, 22 January 2013


Full id: C1399_Bronchial_Tracheal_bronchial_Lymphatic_salivary_Small_lung



Phase1 CAGE Peaks

Hg19::chr14:75033780..75033781,+p@chr14:75033780..75033781
+
Hg19::chr17:38179565..38179597,-p4@MED24
Hg19::chr17:38179600..38179634,-p2@MED24
Hg19::chr17:38179639..38179652,-p7@MED24
Hg19::chr1:95089255..95089279,-p1@ENST00000435559
Hg19::chr6:6803656..6803661,+p@chr6:6803656..6803661
+


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:0042809vitamin D receptor binding0.00964765100671141
GO:0016455RNA polymerase II transcription mediator activity0.00964765100671141
GO:0000119mediator complex0.00964765100671141
GO:0046966thyroid hormone receptor binding0.00964765100671141
GO:0030374ligand-dependent nuclear receptor transcription coactivator activity0.00964765100671141
GO:0030521androgen receptor signaling pathway0.00964765100671141
GO:0016251general RNA polymerase II transcription factor activity0.00964765100671141
GO:0006367transcription initiation from RNA polymerase II promoter0.00964765100671141
GO:0030518steroid hormone receptor signaling pathway0.00964765100671141
GO:0030522intracellular receptor-mediated signaling pathway0.00964765100671141
GO:0035257nuclear hormone receptor binding0.00964765100671141
GO:0051427hormone receptor binding0.00964765100671141
GO:0006352transcription initiation0.0142175909572589
GO:0016591DNA-directed RNA polymerase II, holoenzyme0.0166839077559671
GO:0003713transcription coactivator activity0.0253208524667373
GO:0003702RNA polymerase II transcription factor activity0.0330318466600978
GO:0065004protein-DNA complex assembly0.0330318466600978
GO:0003712transcription cofactor activity0.0330318466600978
GO:0016563transcription activator activity0.0330318466600978
GO:0008134transcription factor binding0.0437166742359254
GO:0044451nucleoplasm part0.0437166742359254
GO:0005654nucleoplasm0.0479151279663466



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
respiratory epithelial cell3.38e-2313
endo-epithelial cell1.62e-2142
epithelial cell4.21e-21253
endodermal cell2.09e-1558
epithelial cell of tracheobronchial tree3.56e-149
epithelial cell of lower respiratory tract3.56e-149
general ecto-epithelial cell1.64e-1014
mammary gland epithelial cell4.34e-104
bronchial epithelial cell3.01e-093
duct epithelial cell3.17e-093
branched duct epithelial cell3.17e-093
tracheal epithelial cell3.17e-093
tracheoblast3.17e-093
gingival epithelial cell2.55e-083
epithelial cell of lung3.76e-0719
epidermal cell4.47e-079
stratified squamous epithelial cell5.17e-076
keratin accumulating cell5.17e-076
stratified epithelial cell5.17e-076
keratinizing barrier epithelial cell5.17e-076
epithelial fate stem cell5.17e-076
stratified epithelial stem cell5.17e-076
surface ectodermal cell5.17e-076
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.22e-17160
endoderm1.22e-17160
presumptive endoderm1.22e-17160
respiratory system1.68e-1774
epithelial bud5.58e-1737
epithelial fold7.07e-1647
respiratory tract3.76e-1554
thoracic cavity element2.62e-1334
thoracic cavity2.62e-1334
tracheobronchial tree6.53e-1315
lower respiratory tract6.53e-1315
thoracic segment organ8.15e-1335
respiratory primordium1.70e-1138
endoderm of foregut1.70e-1138
digestive system5.34e-11145
digestive tract5.34e-11145
primitive gut5.34e-11145
endo-epithelium1.26e-1082
anatomical space1.48e-1095
subdivision of digestive tract2.62e-10118
mammary gland4.34e-104
mammary bud4.34e-104
mammary ridge4.34e-104
mammary placode4.34e-104
trachea1.64e-097
respiratory airway1.64e-097
lung1.85e-0922
respiratory tube1.85e-0922
respiration organ1.85e-0922
pair of lungs1.85e-0922
lung primordium1.85e-0922
lung bud1.85e-0922
lower respiratory tract epithelium3.01e-093
epithelium of bronchus3.01e-093
immaterial anatomical entity7.50e-09117
thoracic segment of trunk1.51e-0852
respiratory system epithelium1.60e-0828
segment of respiratory tract2.29e-0847
gingival epithelium2.55e-083
urothelium4.79e-085
foregut5.45e-0887
respiratory tract epithelium3.76e-0719
lung epithelium3.76e-0719
orifice4.76e-0736


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)
MA0003.10.321379
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.13.85762
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.13.61901
MA0055.10.465994
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.24837
MA0063.10
MA0066.12.69973
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.11.58758
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.11.29635
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.81721
MA0103.11.76074
MA0105.10.134725
MA0106.10.70837
MA0107.11.54633
MA0108.22.01717
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.12.36812
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.569061
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.23.64053
MA0065.21.18263
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.13.32265
MA0155.11.09123
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.11.46233
MA0161.10
MA0162.10.150673
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.476723
MA0102.21.58513
MA0258.13.98052
MA0259.10.893594
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
ESR1#2099315.38430164807720.0006374039095799040.005226491867207
NR3C1#290837.486511665586520.00510866965984070.0237574294507126
STAT3#6774610.51946499715427.37398960627247e-073.26603944227943e-05
TFAP2A#7020616.5186343730454.91595718330683e-083.15755013694577e-06
TFAP2C#7022610.80922860986026.2644941908553e-072.86327137329863e-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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