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Coexpression cluster:C458: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.102469,0.18095,0.0984893,0.54841,0.266493,1.04201,0.239567,0.863457,0.0294929,0.0545264,0.165709,0.748251,0.662693,0.231159,0.264653,0.0881735,0.416635,0.434454,0.0212388,0.153235,1.10741,0.151153,0.180548,0.551194,1.85586,0.289541,0.343036,0.179098,0.0787487,0.147924,0.151697,0.448071,0.0406138,0.21322,0.0614574,0.252623,0.0600845,0.186559,0.420263,0.0244783,0.21951,0.141543,0.181777,0.0758747,0.0127354,0.115453,0.240368,0.158699,0.159934,0.078811,0.300624,0.249086,0.0316867,0.515129,0.653159,0.233295,0.581687,0.209799,0.0544304,0.60157,0.483605,0.242112,0.122235,0.393294,0.255455,0.364726,0.73513,1.08739,0.43915,0.930562,0.133532,0.88957,0.00553467,0.651319,0.017273,0.0146455,0.811576,0.379205,1.11272,0.767791,1.93315,0.392395,0.709459,0.031104,0.604277,0.000162154,1.59428,0.0512809,0.321213,1.18432,0.823081,0.579812,0.462581,0.377714,0.0776122,1.55902,0.0208754,0.499768,0.324895,0.24534,0.0509974,0.45769,0.494867,0.419744,0.355282,0.48954,0.406348,0.228655,0.123981,0.0697646,0.340916,0.492438,0.316828,0.171884,0.777703,0.814512,0.0104292,0.15094,0.362802,0.682586,0.64371,0.319278,0.183912,0.263675,0.882719,0.379837,0.234914,0.466912,0.683004,0.182525,0.580435,0.153507,0.696335,0.26116,0.835304,0.0469425,0.147939,0.530448,0.795107,1.6331,1.23566,0.759951,0.665332,0.496668,0.356718,0.20386,0.343142,1.4753,0.139503,0.0420132,0.0255653,0.00135206,0.58078,0.0271838,0.241755,0.959994,0.308372,0.247915,0.124164,0.107739,0.758809,0.564094,0.435692,0.109525,0.36994,0.254599,0.344454,0.238589,0.000561911
|tfbs_overrepresentation_jaspar=MA0003.1;8.95462e-07,MA0004.1;0.974673,MA0006.1;0.0763783,MA0007.1;0.156885,MA0009.1;0.543169,MA0014.1;1.91579e-05,MA0017.1;0.31911,MA0019.1;0.275941,MA0024.1;0.450307,MA0025.1;0.665335,MA0027.1;2.11401,MA0028.1;0.0843345,MA0029.1;0.467171,MA0030.1;0.457153,MA0031.1;0.401568,MA0038.1;3.59023,MA0040.1;0.472301,MA0041.1;0.535574,MA0042.1;0.938412,MA0043.1;0.543454,MA0046.1;0.533373,MA0048.1;0.00619675,MA0050.1;0.160894,MA0051.1;0.238478,MA0052.1;0.475699,MA0055.1;0.00257143,MA0056.1;0,MA0057.1;0.00555109,MA0058.1;0.110291,MA0059.1;0.109562,MA0060.1;0.85376,MA0061.1;0.0219462,MA0063.1;0,MA0066.1;0.241938,MA0067.1;0.83875,MA0068.1;0.0133711,MA0069.1;0.529912,MA0070.1;0.519883,MA0071.1;0.611515,MA0072.1;0.515863,MA0073.1;2.65925e-08,MA0074.1;0.23792,MA0076.1;0.119431,MA0077.1;1.26861,MA0078.1;0.846104,MA0081.1;0.109654,MA0083.1;0.549943,MA0084.1;1.01907,MA0087.1;0.513678,MA0088.1;0.0366926,MA0089.1;0,MA0090.1;1.30177,MA0091.1;0.170864,MA0092.1;0.448732,MA0093.1;0.566557,MA0095.1;0,MA0098.1;0,MA0100.1;0.252028,MA0101.1;0.0794742,MA0103.1;0.251512,MA0105.1;0.00427625,MA0106.1;0.272934,MA0107.1;0.046982,MA0108.2;1.03141,MA0109.1;0,MA0111.1;0.836455,MA0113.1;1.42179,MA0114.1;0.388646,MA0115.1;0.766188,MA0116.1;0.0483327,MA0117.1;0.577217,MA0119.1;0.676972,MA0122.1;0.600851,MA0124.1;0.727093,MA0125.1;0.648747,MA0130.1;0,MA0131.1;0.329895,MA0132.1;0,MA0133.1;0,MA0135.1;0.570637,MA0136.1;0.246897,MA0139.1;0.0845536,MA0140.1;0.606998,MA0141.1;0.108582,MA0142.1;0.374765,MA0143.1;0.285827,MA0144.1;0.356992,MA0145.1;0.00212809,MA0146.1;1.04313e-05,MA0147.1;0.731862,MA0148.1;0.185927,MA0149.1;0.204488,MA0062.2;0.0205944,MA0035.2;0.210872,MA0039.2;1.7882e-06,MA0138.2;0.316226,MA0002.2;0.0261526,MA0137.2;0.0876366,MA0104.2;0.121334,MA0047.2;0.263601,MA0112.2;0.00179367,MA0065.2;0.0144725,MA0150.1;0.785204,MA0151.1;0,MA0152.1;0.618168,MA0153.1;0.633172,MA0154.1;0.00405158,MA0155.1;0.303035,MA0156.1;0.0888107,MA0157.1;0.352016,MA0158.1;0,MA0159.1;0.049967,MA0160.1;0.571442,MA0161.1;0,MA0162.1;7.59857e-05,MA0163.1;0.0144385,MA0164.1;0.295453,MA0080.2;0.0778984,MA0018.2;0.274004,MA0099.2;0.216352,MA0079.2;4.42144e-14,MA0102.2;1.05522,MA0258.1;0.0364681,MA0259.1;0.196503,MA0442.1;0
}}
}}

Revision as of 19:11, 22 January 2013


Full id: C458_salivary_parietal_middle_locus_medial_occipital_globus



Phase1 CAGE Peaks

Hg19::chr10:105796014..105796053,-p@chr10:105796014..105796053
-
Hg19::chr12:52912957..52912973,-p17@KRT5
Hg19::chr12:52913230..52913233,-p11@KRT5
Hg19::chr13:43059605..43059611,+p@chr13:43059605..43059611
+
Hg19::chr1:209741112..209741127,-p1@ENST00000424696
Hg19::chr1:209741162..209741173,-p2@ENST00000424696
Hg19::chr20:3295706..3295717,-p@chr20:3295706..3295717
-
Hg19::chr20:3295742..3295749,-p@chr20:3295742..3295749
-
Hg19::chr3:48471830..48471839,-p27@PLXNB1
Hg19::chr5:110104185..110104192,-p@chr5:110104185..110104192
-
Hg19::chr5:66942627..66942643,-p1@ENST00000507298
Hg19::chr6:25004699..25004706,-p@chr6:25004699..25004706
-
Hg19::chr6:25004760..25004769,-p@chr6:25004760..25004769
-
Hg19::chr6:25004775..25004790,-p@chr6:25004775..25004790
-
Hg19::chr6:25004791..25004799,-p@chr6:25004791..25004799
-
Hg19::chr6:25004888..25004899,-p@chr6:25004888..25004899
-
Hg19::chr6:56488575..56488587,-p@chr6:56488575..56488587
-
Hg19::chr6:56489323..56489336,-p@chr6:56489323..56489336
-
Hg19::chrM:294..305,+p@chrM:294..305
+
Hg19::chrM:313..339,+p@chrM:313..339
+
Hg19::chrM:408..427,+p@chrM:408..427
+


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:0030215semaphorin receptor binding0.00441540091840339
GO:0017154semaphorin receptor activity0.00662290641421346
GO:0050772positive regulation of axonogenesis0.0176577044057807
GO:0050769positive regulation of neurogenesis0.0176577044057807
GO:0050770regulation of axonogenesis0.0229516363620597
GO:0048731system development0.0239562660080635
GO:0050767regulation of neurogenesis0.0239562660080635
GO:0048856anatomical structure development0.0326402836208885
GO:0051094positive regulation of developmental process0.0333279086719243
GO:0007275multicellular organismal development0.0340768241083792
GO:0005200structural constituent of cytoskeleton0.0340768241083792
GO:0007409axonogenesis0.0349943232195785
GO:0048667neuron morphogenesis during differentiation0.0349943232195785
GO:0048812neurite morphogenesis0.0349943232195785
GO:0000904cellular morphogenesis during differentiation0.0349943232195785
GO:0031175neurite development0.0349943232195785
GO:0008544epidermis development0.0349943232195785
GO:0007398ectoderm development0.0354912267981477
GO:0048666neuron development0.0354912267981477
GO:0032502developmental process0.0354912267981477
GO:0032990cell part morphogenesis0.0354912267981477
GO:0030030cell projection organization and biogenesis0.0354912267981477
GO:0048858cell projection morphogenesis0.0354912267981477
GO:0030182neuron differentiation0.0354912267981477
GO:0032501multicellular organismal process0.0354912267981477
GO:0016477cell migration0.0354912267981477
GO:0050793regulation of developmental process0.0354912267981477
GO:0005882intermediate filament0.0354912267981477
GO:0045111intermediate filament cytoskeleton0.0354912267981477
GO:0048699generation of neurons0.0354912267981477
GO:0022008neurogenesis0.0371739046797585
GO:0009888tissue development0.0418959878611011
GO:0051674localization of cell0.0494585425614447
GO:0006928cell motility0.0494585425614447



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>

Uber Anatomy
Ontology termp-valuen
gland of gut2.66e-2310
saliva-secreting gland1.97e-226
gland of oral region1.97e-226
gland of foregut1.97e-226
oral gland1.97e-226
oral cavity1.97e-226
uterus or analog1.16e-151
oral opening8.18e-1122
uterine cervix1.99e-106
neck of organ1.99e-106
orifice5.48e-1036
respiratory system6.24e-0974
gland1.74e-0859
mouth2.93e-0829
stomodeum2.93e-0829
exocrine gland9.03e-0831
exocrine system9.03e-0831


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)
MA0003.18.95462e-07
MA0004.10.974673
MA0006.10.0763783
MA0007.10.156885
MA0009.10.543169
MA0014.11.91579e-05
MA0017.10.31911
MA0019.10.275941
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.0843345
MA0029.10.467171
MA0030.10.457153
MA0031.10.401568
MA0038.13.59023
MA0040.10.472301
MA0041.10.535574
MA0042.10.938412
MA0043.10.543454
MA0046.10.533373
MA0048.10.00619675
MA0050.10.160894
MA0051.10.238478
MA0052.10.475699
MA0055.10.00257143
MA0056.10
MA0057.10.00555109
MA0058.10.110291
MA0059.10.109562
MA0060.10.85376
MA0061.10.0219462
MA0063.10
MA0066.10.241938
MA0067.10.83875
MA0068.10.0133711
MA0069.10.529912
MA0070.10.519883
MA0071.10.611515
MA0072.10.515863
MA0073.12.65925e-08
MA0074.10.23792
MA0076.10.119431
MA0077.11.26861
MA0078.10.846104
MA0081.10.109654
MA0083.10.549943
MA0084.11.01907
MA0087.10.513678
MA0088.10.0366926
MA0089.10
MA0090.11.30177
MA0091.10.170864
MA0092.10.448732
MA0093.10.566557
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.0794742
MA0103.10.251512
MA0105.10.00427625
MA0106.10.272934
MA0107.10.046982
MA0108.21.03141
MA0109.10
MA0111.10.836455
MA0113.11.42179
MA0114.10.388646
MA0115.10.766188
MA0116.10.0483327
MA0117.10.577217
MA0119.10.676972
MA0122.10.600851
MA0124.10.727093
MA0125.10.648747
MA0130.10
MA0131.10.329895
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.246897
MA0139.10.0845536
MA0140.10.606998
MA0141.10.108582
MA0142.10.374765
MA0143.10.285827
MA0144.10.356992
MA0145.10.00212809
MA0146.11.04313e-05
MA0147.10.731862
MA0148.10.185927
MA0149.10.204488
MA0062.20.0205944
MA0035.20.210872
MA0039.21.7882e-06
MA0138.20.316226
MA0002.20.0261526
MA0137.20.0876366
MA0104.20.121334
MA0047.20.263601
MA0112.20.00179367
MA0065.20.0144725
MA0150.10.785204
MA0151.10
MA0152.10.618168
MA0153.10.633172
MA0154.10.00405158
MA0155.10.303035
MA0156.10.0888107
MA0157.10.352016
MA0158.10
MA0159.10.049967
MA0160.10.571442
MA0161.10
MA0162.17.59857e-05
MA0163.10.0144385
MA0164.10.295453
MA0080.20.0778984
MA0018.20.274004
MA0099.20.216352
MA0079.24.42144e-14
MA0102.21.05522
MA0258.10.0364681
MA0259.10.196503
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
STAT3#677484.007415237011140.0004340408185202020.00405173302157949



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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