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Coexpression cluster:C348: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0423165,0.157768,0.0400013,0.663734,0.282284,0.659968,0.13697,0.230442,0.896661,0.00145175,0.082933,0.488478,0.0639931,0.408634,0.279917,0.137241,0.283109,1.29372,0.494272,0.921334,0.358398,0.166785,0.0933127,0.508482,0.0554737,0.176305,0.218248,0.307965,1.65812,0.689974,0.255613,0.310643,0.776549,0.674305,0.224873,0.0294971,0.0196487,0.0975929,0.361969,0.0291669,1.41105,0.0666551,0.317245,0.2773,0.0235763,0.0500962,0.137585,0.268937,0.276128,0.287898,0.185267,0.144315,0.190863,0.370484,0.497309,0.132172,1.68613,0.367177,0.479389,0.113991,0.342179,0.138926,0.399043,0.262912,0.14927,0.238513,0.574343,0.913986,0.302792,0.761456,0.0614495,0.0406816,0.000558086,0.495593,0.00310636,0.118769,0.510032,0.69939,0.81256,0.196895,1.36826,0.26214,0.149063,0.927139,0.451923,0.000221626,0.0680261,0.0341816,0.20212,1.00897,0.65804,0.429389,0.323471,0.534591,0.118218,2.05384,0.164811,0.356655,0.20516,0.784319,1.6683,0.319139,0.352258,0.285815,0.230532,0.0809099,0.27418,0.403765,0.0553809,0.0243978,0.167208,0.923842,0.0383185,0.0872186,0.614737,0.682395,7.84401e-05,0.0728865,0.236884,0.544542,0.488501,1.10049,0.317215,0.47206,0.715288,0.251373,0.415941,0.327313,0.525232,0.87743,0.429962,0.550129,0.537753,0.153736,0.669744,0.426491,0.906097,0.0925536,0.631317,1.45283,1.05945,0.597865,0.134374,0.353873,0.231743,0.720836,0.220337,1.29622,0.0653198,0.0116437,0.0834127,6.56022e-05,0.430278,0.00611461,0.138651,0.789951,0.559715,1.13594,0.781793,0.0454339,0.596781,0.414981,0.299757,0.176396,0.242939,0.454322,0.137254,0.423097,0.0380941
|tfbs_overrepresentation_for_novel_motifs=0.0423165,0.157768,0.0400013,0.663734,0.282284,0.659968,0.13697,0.230442,0.896661,0.00145175,0.082933,0.488478,0.0639931,0.408634,0.279917,0.137241,0.283109,1.29372,0.494272,0.921334,0.358398,0.166785,0.0933127,0.508482,0.0554737,0.176305,0.218248,0.307965,1.65812,0.689974,0.255613,0.310643,0.776549,0.674305,0.224873,0.0294971,0.0196487,0.0975929,0.361969,0.0291669,1.41105,0.0666551,0.317245,0.2773,0.0235763,0.0500962,0.137585,0.268937,0.276128,0.287898,0.185267,0.144315,0.190863,0.370484,0.497309,0.132172,1.68613,0.367177,0.479389,0.113991,0.342179,0.138926,0.399043,0.262912,0.14927,0.238513,0.574343,0.913986,0.302792,0.761456,0.0614495,0.0406816,0.000558086,0.495593,0.00310636,0.118769,0.510032,0.69939,0.81256,0.196895,1.36826,0.26214,0.149063,0.927139,0.451923,0.000221626,0.0680261,0.0341816,0.20212,1.00897,0.65804,0.429389,0.323471,0.534591,0.118218,2.05384,0.164811,0.356655,0.20516,0.784319,1.6683,0.319139,0.352258,0.285815,0.230532,0.0809099,0.27418,0.403765,0.0553809,0.0243978,0.167208,0.923842,0.0383185,0.0872186,0.614737,0.682395,7.84401e-05,0.0728865,0.236884,0.544542,0.488501,1.10049,0.317215,0.47206,0.715288,0.251373,0.415941,0.327313,0.525232,0.87743,0.429962,0.550129,0.537753,0.153736,0.669744,0.426491,0.906097,0.0925536,0.631317,1.45283,1.05945,0.597865,0.134374,0.353873,0.231743,0.720836,0.220337,1.29622,0.0653198,0.0116437,0.0834127,6.56022e-05,0.430278,0.00611461,0.138651,0.789951,0.559715,1.13594,0.781793,0.0454339,0.596781,0.414981,0.299757,0.176396,0.242939,0.454322,0.137254,0.423097,0.0380941
|tfbs_overrepresentation_jaspar=MA0003.1;0.000945872,MA0004.1;1.01395,MA0006.1;0.279119,MA0007.1;0.265481,MA0009.1;0.395891,MA0014.1;7.29465e-05,MA0017.1;0.152238,MA0019.1;0.165418,MA0024.1;0.840207,MA0025.1;0.508683,MA0027.1;1.93196,MA0028.1;0.032054,MA0029.1;0.873668,MA0030.1;1.54061,MA0031.1;0.270046,MA0038.1;0.846563,MA0040.1;1.58836,MA0041.1;0.0940493,MA0042.1;0.272024,MA0043.1;0.39615,MA0046.1;0.386991,MA0048.1;0.48774,MA0050.1;0.575427,MA0051.1;0.422881,MA0052.1;0.335128,MA0055.1;0.0659955,MA0056.1;0,MA0057.1;0.0170157,MA0058.1;1.09049,MA0059.1;1.08504,MA0060.1;0.0369498,MA0061.1;0.0254374,MA0063.1;0,MA0066.1;0.429622,MA0067.1;0.673046,MA0068.1;0.770311,MA0069.1;0.383853,MA0070.1;0.374777,MA0071.1;1.23187,MA0072.1;0.371146,MA0073.1;1.88627e-07,MA0074.1;0.421793,MA0076.1;0.0525452,MA0077.1;1.70358,MA0078.1;0.573222,MA0081.1;0.176635,MA0083.1;2.74237,MA0084.1;0.847335,MA0087.1;0.966048,MA0088.1;0.0126425,MA0089.1;0,MA0090.1;0.461949,MA0091.1;0.609422,MA0092.1;0.525602,MA0093.1;0.526085,MA0095.1;0,MA0098.1;0,MA0100.1;0.146599,MA0101.1;0.029437,MA0103.1;0.108135,MA0105.1;0.0125892,MA0106.1;0.490178,MA0107.1;0.0137208,MA0108.2;0.267801,MA0109.1;0,MA0111.1;0.845209,MA0113.1;0.173209,MA0114.1;0.0617658,MA0115.1;0.603788,MA0116.1;0.875375,MA0117.1;0.427006,MA0119.1;0.36594,MA0122.1;0.44876,MA0124.1;0.566745,MA0125.1;0.493194,MA0130.1;0,MA0131.1;0.2093,MA0132.1;0,MA0133.1;0,MA0135.1;1.07934,MA0136.1;0.142619,MA0139.1;0.279308,MA0140.1;0.115685,MA0141.1;0.393986,MA0142.1;0.247045,MA0143.1;0.99178,MA0144.1;0.0531404,MA0145.1;0.00552415,MA0146.1;0.0173024,MA0147.1;1.24352,MA0148.1;0.0971411,MA0149.1;0.110599,MA0062.2;0.004042,MA0035.2;0.11531,MA0039.2;2.70061e-06,MA0138.2;1.09061,MA0002.2;0.0936468,MA0137.2;0.3196,MA0104.2;0.894353,MA0047.2;0.155654,MA0112.2;0.0364067,MA0065.2;0.0921185,MA0150.1;0.0556869,MA0151.1;0,MA0152.1;0.761762,MA0153.1;2.09024,MA0154.1;0.145314,MA0155.1;0.0122069,MA0156.1;0.0345163,MA0157.1;0.227782,MA0158.1;0,MA0159.1;0.597825,MA0160.1;1.68729,MA0161.1;0,MA0162.1;0.00039512,MA0163.1;0.000379398,MA0164.1;0.181076,MA0080.2;0.284607,MA0018.2;0.163878,MA0099.2;0.119388,MA0079.2;7.33039e-07,MA0102.2;0.88257,MA0258.1;1.37581,MA0259.1;0.378383,MA0442.1;0
}}
}}

Revision as of 19:05, 22 January 2013


Full id: C348_Melanocyte_melanoma_retina_cervical_eye_carcinoid_Basophils



Phase1 CAGE Peaks

Hg19::chr12:85380577..85380591,+p@chr12:85380577..85380591
+
Hg19::chr12:85380634..85380663,+p@chr12:85380634..85380663
+
Hg19::chr14:34638804..34638809,-p@chr14:34638804..34638809
-
Hg19::chr14:34638833..34638843,-p@chr14:34638833..34638843
-
Hg19::chr14:34638855..34638875,-p@chr14:34638855..34638875
-
Hg19::chr15:28000407..28000435,+p@chr15:28000407..28000435
+
Hg19::chr15:42686298..42686307,+p@chr15:42686298..42686307
+
Hg19::chr15:42686326..42686331,+p@chr15:42686326..42686331
+
Hg19::chr15:42686383..42686405,+p@chr15:42686383..42686405
+
Hg19::chr15:55562451..55562456,-p15@RAB27A
Hg19::chr16:84074687..84074692,+p@chr16:84074687..84074692
+
Hg19::chr16:84074748..84074755,+p@chr16:84074748..84074755
+
Hg19::chr16:84076377..84076384,-p@chr16:84076377..84076384
-
Hg19::chr16:84076394..84076415,-p@chr16:84076394..84076415
-
Hg19::chr16:84076419..84076439,-p@chr16:84076419..84076439
-
Hg19::chr19:34566680..34566687,-p@chr19:34566680..34566687
-
Hg19::chr19:34566717..34566729,-p@chr19:34566717..34566729
-
Hg19::chr1:1497417..1497420,-p5@AK129493
Hg19::chr1:76559872..76559889,+p@chr1:76559872..76559889
+
Hg19::chr20:20066107..20066120,+p3@C20orf26
Hg19::chr21:44751903..44751935,-p3@LINC00322
Hg19::chr21:44751988..44752030,-p1@LINC00322
Hg19::chr2:12531762..12531779,+p@chr2:12531762..12531779
+
Hg19::chr6:4613693..4613698,-p@chr6:4613693..4613698
-
Hg19::chr7:107338327..107338350,+p@chr7:107338327..107338350
+
Hg19::chr7:2657383..2657390,-p@chr7:2657383..2657390
-
Hg19::chr7:2657395..2657398,-p@chr7:2657395..2657398
-
Hg19::chr8:29605917..29605922,+p6@ENST00000517491
Hg19::chr9:12693559..12693562,+p22@TYRP1
Hg19::chr9:12693574..12693586,+p4@TYRP1
Hg19::chr9:12712278..12712297,+p@chr9:12712278..12712297
+
Hg19::chr9:15852076..15852082,+p@chr9:15852076..15852082
+


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:0048770pigment granule0.000803718988714016
GO:0042470melanosome0.000803718988714016
GO:0016023cytoplasmic membrane-bound vesicle0.00432632868103671
GO:0031988membrane-bound vesicle0.00432632868103671
GO:0031410cytoplasmic vesicle0.00432632868103671
GO:0031982vesicle0.00432632868103671
GO:0006583melanin biosynthetic process from tyrosine0.00432632868103671
GO:0016743carboxyl- or carbamoyltransferase activity0.00432632868103671
GO:0033162melanosome membrane0.00432632868103671
GO:0042438melanin biosynthetic process0.00432632868103671
GO:0045009chitosome0.00432632868103671
GO:0006520amino acid metabolic process0.00432632868103671
GO:0006582melanin metabolic process0.00432632868103671
GO:0006519amino acid and derivative metabolic process0.0050106529745457
GO:0009308amine metabolic process0.0062897768722019
GO:0006807nitrogen compound metabolic process0.00669624608822885
GO:0006570tyrosine metabolic process0.00708769263159723
GO:0019752carboxylic acid metabolic process0.0077947622951902
GO:0006082organic acid metabolic process0.0077947622951902
GO:0016597amino acid binding0.00803153590929619
GO:0046148pigment biosynthetic process0.0138653021754353
GO:0030425dendrite0.0138653021754353
GO:0042440pigment metabolic process0.0146567851033241
GO:0043176amine binding0.0147140802849302
GO:0009072aromatic amino acid family metabolic process0.0150872874889512
GO:0019748secondary metabolic process0.0163560750641171
GO:0043005neuron projection0.0240513596851761
GO:0046982protein heterodimerization activity0.0285724975268364
GO:0030659cytoplasmic vesicle membrane0.0285724975268364
GO:0044433cytoplasmic vesicle part0.0285724975268364
GO:0012506vesicle membrane0.0291961537523382
GO:0005507copper ion binding0.029281517566322
GO:0042803protein homodimerization activity0.0382979900861493
GO:0006725aromatic compound metabolic process0.0430214324378555



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
retina9.49e-076
photoreceptor array9.49e-076
posterior segment of eyeball9.49e-076


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)
MA0003.10.000945872
MA0004.11.01395
MA0006.10.279119
MA0007.10.265481
MA0009.10.395891
MA0014.17.29465e-05
MA0017.10.152238
MA0019.10.165418
MA0024.10.840207
MA0025.10.508683
MA0027.11.93196
MA0028.10.032054
MA0029.10.873668
MA0030.11.54061
MA0031.10.270046
MA0038.10.846563
MA0040.11.58836
MA0041.10.0940493
MA0042.10.272024
MA0043.10.39615
MA0046.10.386991
MA0048.10.48774
MA0050.10.575427
MA0051.10.422881
MA0052.10.335128
MA0055.10.0659955
MA0056.10
MA0057.10.0170157
MA0058.11.09049
MA0059.11.08504
MA0060.10.0369498
MA0061.10.0254374
MA0063.10
MA0066.10.429622
MA0067.10.673046
MA0068.10.770311
MA0069.10.383853
MA0070.10.374777
MA0071.11.23187
MA0072.10.371146
MA0073.11.88627e-07
MA0074.10.421793
MA0076.10.0525452
MA0077.11.70358
MA0078.10.573222
MA0081.10.176635
MA0083.12.74237
MA0084.10.847335
MA0087.10.966048
MA0088.10.0126425
MA0089.10
MA0090.10.461949
MA0091.10.609422
MA0092.10.525602
MA0093.10.526085
MA0095.10
MA0098.10
MA0100.10.146599
MA0101.10.029437
MA0103.10.108135
MA0105.10.0125892
MA0106.10.490178
MA0107.10.0137208
MA0108.20.267801
MA0109.10
MA0111.10.845209
MA0113.10.173209
MA0114.10.0617658
MA0115.10.603788
MA0116.10.875375
MA0117.10.427006
MA0119.10.36594
MA0122.10.44876
MA0124.10.566745
MA0125.10.493194
MA0130.10
MA0131.10.2093
MA0132.10
MA0133.10
MA0135.11.07934
MA0136.10.142619
MA0139.10.279308
MA0140.10.115685
MA0141.10.393986
MA0142.10.247045
MA0143.10.99178
MA0144.10.0531404
MA0145.10.00552415
MA0146.10.0173024
MA0147.11.24352
MA0148.10.0971411
MA0149.10.110599
MA0062.20.004042
MA0035.20.11531
MA0039.22.70061e-06
MA0138.21.09061
MA0002.20.0936468
MA0137.20.3196
MA0104.20.894353
MA0047.20.155654
MA0112.20.0364067
MA0065.20.0921185
MA0150.10.0556869
MA0151.10
MA0152.10.761762
MA0153.12.09024
MA0154.10.145314
MA0155.10.0122069
MA0156.10.0345163
MA0157.10.227782
MA0158.10
MA0159.10.597825
MA0160.11.68729
MA0161.10
MA0162.10.00039512
MA0163.10.000379398
MA0164.10.181076
MA0080.20.284607
MA0018.20.163878
MA0099.20.119388
MA0079.27.33039e-07
MA0102.20.88257
MA0258.11.37581
MA0259.10.378383
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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