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Coexpression cluster:C208: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0980489,0.268254,0.00157614,0.295561,0.21097,0.499633,0.235016,3.05976,0.764919,0.00489314,0.00766346,0.296721,0.0143638,0.0873197,0.500793,1.71161,0.294554,3.02173,0.0768545,0.103143,0.477763,0.0796379,0.0493303,0.20037,0.265481,0.331647,0.471698,0.133831,0.120983,0.272685,0.0952051,0.337528,0.319883,0.358947,0.0117646,0.07625,0.0321762,0.0533175,1.26673,0.0263022,1.21214,0.0271672,0.295666,1.81896,0.0708298,0.0160908,0.095256,0.104581,0.722852,0.0575853,0.354367,0.252623,0.0279062,0.140793,0.230934,0.0891337,1.58145,0.0700906,0.965456,0.18155,0.12258,0.0967921,0.131058,0.0763164,0.0257254,0.227828,1.44134,0.585626,0.325152,0.448739,0.0234395,1.27793,1.20659e-05,0.229635,4.70601e-06,0.641507,0.686259,0.52626,0.660881,0.0580631,0.315867,0.0759041,0.264122,0.330522,0.19725,1.04227e-11,0.00566505,0.344888,0.176583,0.673436,0.359856,1.02318,1.19176,0.492096,0.00547598,0.747851,0.197155,0.131795,0.40555,0.184333,2.20562,0.108371,0.404604,0.298724,0.216317,0.110193,0.0824191,0.413644,0.141532,0.0161389,0.199249,0.127583,0.170654,0.123169,0.865442,0.517459,0.0019563,0.0942132,0.842958,1.38342,0.224287,0.174415,0.287551,0.519536,1.05242,0.246666,1.0375,0.364112,0.702854,0.402017,0.53533,0.373057,1.33504,0.511756,0.369719,0.0603673,0.196059,2.22369,0.895994,1.09888,0.72072,0.310069,1.43539,0.130007,0.218055,0.342311,0.201829,0.94671,0.32071,0.0743242,0.0178829,1.35287e-08,0.181711,0.06462,0.022187,0.473848,0.66169,0.182686,0.141923,0.0451616,0.309187,0.170952,0.0968812,0.0468716,0.0659297,0.491575,0.419382,0.443118,0.000701234
|tfbs_overrepresentation_jaspar=MA0003.1;5.39061e-06,MA0004.1;0.248711,MA0006.1;0.0539278,MA0007.1;1.19173,MA0009.1;0.477238,MA0014.1;2.2451e-07,MA0017.1;0.0350052,MA0019.1;0.304367,MA0024.1;0.104455,MA0025.1;0.239591,MA0027.1;1.57122,MA0028.1;0.00690011,MA0029.1;0.364481,MA0030.1;0.711434,MA0031.1;0.5781,MA0038.1;0.0963578,MA0040.1;1.78901,MA0041.1;0.7398,MA0042.1;1.22149,MA0043.1;0.477676,MA0046.1;0.902761,MA0048.1;0.0547545,MA0050.1;0.037344,MA0051.1;0.0213827,MA0052.1;0.757171,MA0055.1;0.144094,MA0056.1;0,MA0057.1;0.0025996,MA0058.1;0.218128,MA0059.1;0.551199,MA0060.1;0.075025,MA0061.1;0.135896,MA0063.1;0,MA0066.1;0.734376,MA0067.1;0.372511,MA0068.1;0.0345442,MA0069.1;0.456987,MA0070.1;0.441823,MA0071.1;0.612705,MA0072.1;1.38431,MA0073.1;1.45187e-08,MA0074.1;0.232012,MA0076.1;0.0175809,MA0077.1;0.425495,MA0078.1;0.684115,MA0081.1;0.216008,MA0083.1;0.945431,MA0084.1;1.30291,MA0087.1;1.37635,MA0088.1;0.00520972,MA0089.1;0,MA0090.1;0.676012,MA0091.1;0.681327,MA0092.1;0.550211,MA0093.1;0.213609,MA0095.1;0,MA0098.1;0,MA0100.1;0.105723,MA0101.1;0.220746,MA0103.1;0.307392,MA0105.1;0.0165167,MA0106.1;0.548397,MA0107.1;0.72892,MA0108.2;19.5904,MA0109.1;0,MA0111.1;0.308642,MA0113.1;0.925974,MA0114.1;0.0167514,MA0115.1;0.314897,MA0116.1;0.400282,MA0117.1;0.530249,MA0119.1;0.0946406,MA0122.1;0.194957,MA0124.1;0.284987,MA0125.1;1.87738,MA0130.1;0,MA0131.1;0.0497779,MA0132.1;0,MA0133.1;0,MA0135.1;2.25992,MA0136.1;0.755766,MA0139.1;0.0153955,MA0140.1;0.185398,MA0141.1;0.0459652,MA0142.1;0.516104,MA0143.1;0.138563,MA0144.1;0.204128,MA0145.1;0.0172683,MA0146.1;0.000573525,MA0147.1;0.176288,MA0148.1;1.85169,MA0149.1;0.0139923,MA0062.2;0.000608214,MA0035.2;0.362138,MA0039.2;2.09307e-05,MA0138.2;1.06294,MA0002.2;1.56564,MA0137.2;0.257564,MA0104.2;0.0740062,MA0047.2;0.280225,MA0112.2;0.0129327,MA0065.2;0.0337018,MA0150.1;0.651998,MA0151.1;0,MA0152.1;0.377089,MA0153.1;0.216949,MA0154.1;0.793662,MA0155.1;0.280895,MA0156.1;0.0736459,MA0157.1;0.464842,MA0158.1;0,MA0159.1;0.582744,MA0160.1;0.0602046,MA0161.1;0,MA0162.1;6.18999e-07,MA0163.1;3.69363e-06,MA0164.1;0.0376527,MA0080.2;0.344549,MA0018.2;0.126669,MA0099.2;0.625565,MA0079.2;4.82164e-17,MA0102.2;0.556972,MA0258.1;0.277404,MA0259.1;0.0244326,MA0442.1;0
}}
}}

Revision as of 18:43, 22 January 2013


Full id: C208_skin_amniotic_papillotubular_salivary_umbilical_Alveolar_serous



Phase1 CAGE Peaks

Hg19::chr10:94301107..94301111,-p18@IDE
Hg19::chr11:105010477..105010516,-p1@CARD18
Hg19::chr11:65779425..65779509,+p1@CST6
Hg19::chr11:65779676..65779683,+p12@CST6
Hg19::chr12:52685312..52685319,-p11@KRT81
Hg19::chr12:52695617..52695623,+p4@KRT86
Hg19::chr12:52715179..52715182,-p1@KRT83
Hg19::chr12:52761262..52761267,-p1@KRT85
Hg19::chr12:52946923..52946931,-p1@KRT71
Hg19::chr12:52967622..52967628,-p1@KRT74
Hg19::chr12:52995291..52995294,-p5@KRT72
Hg19::chr12:53097305..53097310,-p1@KRT77
Hg19::chr12:53228091..53228096,-p1@KRT79
Hg19::chr16:56598984..56598990,+p1@MT4
Hg19::chr17:20687950..20687982,+p1@SCDP1
Hg19::chr17:38911580..38911584,-p1@KRT25
Hg19::chr17:38938796..38938803,-p1@KRT27
Hg19::chr17:38956205..38956214,-p1@KRT28
Hg19::chr17:39165376..39165381,-p1@KRTAP3-1
Hg19::chr17:39191123..39191127,-p1@KRTAP1-3
Hg19::chr17:39254391..39254395,-p1@KRTAP4-8
Hg19::chr17:39274621..39274626,-p1@KRTAP4-11
Hg19::chr17:39280430..39280436,-p1@KRTAP4-12
Hg19::chr17:39296794..39296798,-p1@KRTAP4-6
Hg19::chr17:39306068..39306077,-p1@KRTAP4-5
Hg19::chr17:39316998..39317001,-p1@KRTAP4-4
Hg19::chr17:39324471..39324474,-p1@KRTAP4-3
Hg19::chr17:39334471..39334474,-p1@KRTAP4-2
Hg19::chr17:39341160..39341165,-p1@KRTAP4-1
Hg19::chr17:39388700..39388702,+p1@KRTAP9-3
p1@KRTAP9-9
Hg19::chr17:39394250..39394253,+p1@KRTAP9-8
Hg19::chr17:39465536..39465562,-p1@KRTAP16-1
Hg19::chr17:39471958..39471963,-p1@KRTAP17-1
Hg19::chr17:39507076..39507080,-p1@KRT33A
Hg19::chr17:39553852..39553863,-p1@KRT31
Hg19::chr17:39637401..39637404,-p1@KRT35
Hg19::chr17:48261972..48261979,-p@chr17:48261972..48261979
-
Hg19::chr17:48262782..48262783,-p55@COL1A1
Hg19::chr18:61209598..61209607,+p@chr18:61209598..61209607
+
Hg19::chr18:61209634..61209647,+p@chr18:61209634..61209647
+
Hg19::chr18:61209658..61209665,+p@chr18:61209658..61209665
+
Hg19::chr19:24140738..24140740,-p1@uc002nrp.1
Hg19::chr19:46753446..46753471,-p@chr19:46753446..46753471
-
Hg19::chr1:152061537..152061542,-p1@TCHHL1
Hg19::chr1:152087919..152087921,-p1@TCHH
Hg19::chr1:152286909..152286919,-p2@FLG
Hg19::chr1:152287109..152287120,-p3@FLG
Hg19::chr1:152332480..152332484,-p1@FLG2
Hg19::chr1:152483278..152483280,+p1@LCE5A
Hg19::chr1:152627927..152627931,+p1@LINC00302
Hg19::chr1:152635854..152635860,+p1@LCE2D
Hg19::chr1:152691067..152691070,+p1@C1orf68
Hg19::chr1:152815327..152815336,+p1@LCE6A
Hg19::chr1:152943122..152943128,+p1@SPRR4
Hg19::chr1:153232160..153232165,+p1@LOR
Hg19::chr1:153522562..153522578,-p11@S100A4
Hg19::chr1:1567038..1567075,+p4@MMP23B
Hg19::chr1:179242347..179242350,+p@chr1:179242347..179242350
+
Hg19::chr21:31655265..31655269,-p1@KRTAP24-1
Hg19::chr21:31852683..31852688,-p1@KRTAP19-1
Hg19::chr21:31874456..31874461,-p1@KRTAP19-5
Hg19::chr21:32185588..32185592,-p1@KRTAP8-1
Hg19::chr21:32202074..32202079,-p1@KRTAP7-1
Hg19::chr21:32253891..32253899,-p1@KRTAP11-1
Hg19::chr21:45978676..45978679,-p1@KRTAP10-3
Hg19::chr21:46047009..46047014,+p1@KRTAP10-9
Hg19::chr21:46132193..46132201,-p@chr21:46132193..46132201
-
Hg19::chr2:189849488..189849548,+p@chr2:189849488..189849548
+
Hg19::chr3:100238112..100238123,+p9@TMEM45A
Hg19::chr4:7436623..7436650,-p1@PSAPL1
Hg19::chr5:132460176..132460179,-p@chr5:132460176..132460179
-
Hg19::chr6:169582924..169582941,-p1@uc011egv.1
Hg19::chr6:31106840..31106848,-p1@PSORS1C2
Hg19::chr8:82373809..82373815,-p1@FABP9


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:0005882intermediate filament1.1208404948315e-59
GO:0045111intermediate filament cytoskeleton1.1208404948315e-59
GO:0044430cytoskeletal part3.9119482783705e-39
GO:0005856cytoskeleton5.76371606942739e-38
GO:0044446intracellular organelle part2.17698466243593e-29
GO:0044422organelle part2.25177511944484e-29
GO:0043232intracellular non-membrane-bound organelle7.68133773291025e-27
GO:0043228non-membrane-bound organelle7.68133773291025e-27
GO:0045095keratin filament1.45046114508371e-17
GO:0008544epidermis development2.26158647486084e-15
GO:0007398ectoderm development4.96550089454214e-15
GO:0009888tissue development1.54617141935801e-11
GO:0043229intracellular organelle6.11875480359721e-10
GO:0043226organelle6.11875480359721e-10
GO:0044424intracellular part1.04983647492565e-09
GO:0031424keratinization3.47712308664615e-08
GO:0009913epidermal cell differentiation1.22758567921542e-07
GO:0048730epidermis morphogenesis2.10050284994915e-07
GO:0005622intracellular3.24635649567415e-07
GO:0048729tissue morphogenesis7.45577359694037e-07
GO:0048513organ development7.940099712924e-06
GO:0032502developmental process9.57971456732683e-05
GO:0048731system development0.000170398828538472
GO:0048856anatomical structure development0.000251224646956548
GO:0007275multicellular organismal development0.000866833468931428
GO:0001533cornified envelope0.00280408857071443
GO:0009653anatomical structure morphogenesis0.00539239046622906
GO:0004231insulysin activity0.00774612961119495
GO:0044464cell part0.0149983939589835
GO:0005584collagen type I0.0201504240562489
GO:0008147structural constituent of bone0.0248826537274661
GO:0005200structural constituent of cytoskeleton0.0287101500655512
GO:0009898internal side of plasma membrane0.0332171421029089
GO:0032501multicellular organismal process0.0465018647410683



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
surface1.23e-661
chest muscle4.66e-661
respiratory system muscle4.66e-661
skeletal muscle of trunk4.66e-661
respiratory system skeletal muscle4.66e-661
thoracic segment muscle4.66e-661
chest organ4.66e-661
muscle of trunk4.66e-661
diaphragm4.66e-661
future diaphragm4.66e-661
muscle structure7.05e-342
muscle organ7.05e-342
zone of skin7.35e-184
umbilical cord6.13e-0810
blastocyst6.13e-0810
blastula6.13e-0810
bilaminar disc6.13e-0810
inner cell mass6.13e-0810
cleaving embryo6.13e-0810
connecting stalk6.13e-0810
inner cell mass derived epiblast6.13e-0810
extraembryonic mesoderm6.13e-0810
chest2.63e-0711


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)
MA0003.15.39061e-06
MA0004.10.248711
MA0006.10.0539278
MA0007.11.19173
MA0009.10.477238
MA0014.12.2451e-07
MA0017.10.0350052
MA0019.10.304367
MA0024.10.104455
MA0025.10.239591
MA0027.11.57122
MA0028.10.00690011
MA0029.10.364481
MA0030.10.711434
MA0031.10.5781
MA0038.10.0963578
MA0040.11.78901
MA0041.10.7398
MA0042.11.22149
MA0043.10.477676
MA0046.10.902761
MA0048.10.0547545
MA0050.10.037344
MA0051.10.0213827
MA0052.10.757171
MA0055.10.144094
MA0056.10
MA0057.10.0025996
MA0058.10.218128
MA0059.10.551199
MA0060.10.075025
MA0061.10.135896
MA0063.10
MA0066.10.734376
MA0067.10.372511
MA0068.10.0345442
MA0069.10.456987
MA0070.10.441823
MA0071.10.612705
MA0072.11.38431
MA0073.11.45187e-08
MA0074.10.232012
MA0076.10.0175809
MA0077.10.425495
MA0078.10.684115
MA0081.10.216008
MA0083.10.945431
MA0084.11.30291
MA0087.11.37635
MA0088.10.00520972
MA0089.10
MA0090.10.676012
MA0091.10.681327
MA0092.10.550211
MA0093.10.213609
MA0095.10
MA0098.10
MA0100.10.105723
MA0101.10.220746
MA0103.10.307392
MA0105.10.0165167
MA0106.10.548397
MA0107.10.72892
MA0108.219.5904
MA0109.10
MA0111.10.308642
MA0113.10.925974
MA0114.10.0167514
MA0115.10.314897
MA0116.10.400282
MA0117.10.530249
MA0119.10.0946406
MA0122.10.194957
MA0124.10.284987
MA0125.11.87738
MA0130.10
MA0131.10.0497779
MA0132.10
MA0133.10
MA0135.12.25992
MA0136.10.755766
MA0139.10.0153955
MA0140.10.185398
MA0141.10.0459652
MA0142.10.516104
MA0143.10.138563
MA0144.10.204128
MA0145.10.0172683
MA0146.10.000573525
MA0147.10.176288
MA0148.11.85169
MA0149.10.0139923
MA0062.20.000608214
MA0035.20.362138
MA0039.22.09307e-05
MA0138.21.06294
MA0002.21.56564
MA0137.20.257564
MA0104.20.0740062
MA0047.20.280225
MA0112.20.0129327
MA0065.20.0337018
MA0150.10.651998
MA0151.10
MA0152.10.377089
MA0153.10.216949
MA0154.10.793662
MA0155.10.280895
MA0156.10.0736459
MA0157.10.464842
MA0158.10
MA0159.10.582744
MA0160.10.0602046
MA0161.10
MA0162.16.18999e-07
MA0163.13.69363e-06
MA0164.10.0376527
MA0080.20.344549
MA0018.20.126669
MA0099.20.625565
MA0079.24.82164e-17
MA0102.20.556972
MA0258.10.277404
MA0259.10.0244326
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

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