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Coexpression cluster:C420: Difference between revisions

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{{Coexpression_clusters
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cell differentiation!0.000349270608805736!353135;353137$GO:0048730!epidermis morphogenesis!0.000349270608805736!353135;353137$GO:0048729!tissue morphogenesis!0.000450575533477953!353135;353137$GO:0008544!epidermis development!0.0012403453005068!353135;353137$GO:0007398!ectoderm development!0.0012403453005068!353135;353137$GO:0009888!tissue development!0.00462729906663375!353135;353137$GO:0006898!receptor-mediated endocytosis!0.0409613735985991!4481$GO:0009653!anatomical structure morphogenesis!0.0412754389292683!353135;353137$GO:0048513!organ 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102632,0.870867,0.286421,0.553496,0.512645,0.192953,0.778399,0.749389,0.920474,0.445744,0.919886,0.000257386,0.145387,0.203306,0.745614,0.308104,0.676308,0.841961,0.0302929|tfbs_overrepresentation_for_novel_motifs=0.0799767,0.0280497,0.0765276,0.471537,0.212185,0.914111,0.204171,0.225126,1.40345,0.0101458,0.136211,0.23459,0.30609,0.196345,1.21907,0.514176,0.372343,0.34735,0.33879,0.100164,0.264528,0.173527,0.149707,0.788708,0.325988,1.29397,0.254373,0.148383,0.215908,0.605585,0.390674,0.402677,0.117917,0.155145,0.0451802,0.0889903,0.04405,0.155199,0.334646,0.0160107,0.170767,0.114449,0.504679,0.796164,0.725277,0.0913173,0.204918,0.129869,0.641077,0.471649,0.261519,0.213054,0.138368,0.467708,0.602614,0.198331,0.0614355,0.523348,0.38523,0.175903,0.437087,0.206544,0.424001,0.349892,0.21901,0.32251,0.683218,1.032,0.394058,0.876356,0.107303,0.235228,0.0581038,0.600809,0.053293,0.455591,0.232053,0.336375,0.39137,0.317476,0.351556,0.34903,1.17144,0.230083,0.554704,0.000526382,0.00178341,0.206868,0.281033,1.1284,0.769994,0.530777,0.416714,1.69141,1.22875,1.32468,0.168495,0.452776,0.284531,0.173006,0.955648,0.41198,0.448017,0.375338,0.313482,0.133549,0.36244,0.194019,0.325637,0.0520752,0.279145,0.445659,0.0739965,0.141815,0.725188,0.0434964,0.000973813,0.388916,0.32067,0.554632,1.44717,2.14491,0.906976,0.226712,0.828974,0.33698,0.199838,0.420907,0.631927,0.324536,0.531386,0.394876,0.645033,1.19293,0.782074,0.192202,0.381933,0.454639,0.742365,1.57584,1.1795,0.707679,0.201014,0.449766,0.314855,0.509971,0.301898,1.41836,0.112626,0.029465,0.115484,0.000592115,0.531723,0.207168,0.20621,0.90553,0.740891,0.195716,0.669214,0.0845645,0.706553,0.515425,0.390719,0.291122,0.3275,0.218208,0.0261345,0.587697,0.000131758|tfbs_overrepresentation_jaspar=MA0003.1;3.13302e-05,MA0004.1;0.430931,MA0006.1;0.0576274,MA0007.1;0.801773,MA0009.1;0.495012,MA0014.1;0.00150727,MA0017.1;0.0747264,MA0019.1;1.24577,MA0024.1;0.404839,MA0025.1;0.614568,MA0027.1;2.05626,MA0028.1;0.0643724,MA0029.1;0.421158,MA0030.1;0.41146,MA0031.1;0.357843,MA0038.1;0.594428,MA0040.1;0.426128,MA0041.1;0.150655,MA0042.1;0.131332,MA0043.1;0.495289,MA0046.1;0.485466,MA0048.1;0.443269,MA0050.1;0.131853,MA0051.1;0.203156,MA0052.1;0.429421,MA0055.1;0.49738,MA0056.1;0,MA0057.1;0.0582452,MA0058.1;0.292964,MA0059.1;0.291213,MA0060.1;0.221405,MA0061.1;0.870948,MA0063.1;0,MA0066.1;0.206381,MA0067.1;0.78548,MA0068.1;0.0418736,MA0069.1;0.482095,MA0070.1;0.472333,MA0071.1;0.179775,MA0072.1;0.468422,MA0073.1;0.0233654,MA0074.1;0.202636,MA0076.1;0.094817,MA0077.1;0.461731,MA0078.1;0.275364,MA0081.1;0.6081,MA0083.1;0.501617,MA0084.1;0.964138,MA0087.1;0.466297,MA0088.1;0.499444,MA0089.1;0,MA0090.1;1.13384,MA0091.1;0.856604,MA0092.1;0.378282,MA0093.1;0.213685,MA0095.1;0,MA0098.1;0,MA0100.1;0.215803,MA0101.1;0.821369,MA0103.1;0.198896,MA0105.1;0.362357,MA0106.1;0.235406,MA0107.1;0.577353,MA0108.2;0.355343,MA0109.1;0,MA0111.1;0.109681,MA0113.1;0.247415,MA0114.1;0.306489,MA0115.1;0.71383,MA0116.1;0.588414,MA0117.1;0.528241,MA0119.1;0.569272,MA0122.1;1.35859,MA0124.1;0.675302,MA0125.1;1.45755,MA0130.1;0,MA0131.1;0.289284,MA0132.1;0,MA0133.1;0,MA0135.1;0.521813,MA0136.1;1.14145,MA0139.1;0.0119363,MA0140.1;0.178014,MA0141.1;0.0853004,MA0142.1;0.33212,MA0143.1;0.247545,MA0144.1;1.196,MA0145.1;0.00708665,MA0146.1;2.28252e-06,MA0147.1;0.330796,MA0148.1;0.469347,MA0149.1;0.17166,MA0062.2;0.0628366,MA0035.2;0.177548,MA0039.2;0.000705892,MA0138.2;0.276299,MA0002.2;0.642982,MA0137.2;0.511766,MA0104.2;0.0196756,MA0047.2;0.226642,MA0112.2;0.022609,MA0065.2;0.145654,MA0150.1;0.0992631,MA0151.1;0,MA0152.1;0.537486,MA0153.1;0.583009,MA0154.1;0.537265,MA0155.1;0.0527191,MA0156.1;0.885166,MA0157.1;0.835144,MA0158.1;0,MA0159.1;0.0358122,MA0160.1;0.164277,MA0161.1;0,MA0162.1;0.00132146,MA0163.1;0.0056464,MA0164.1;0.712784,MA0080.2;1.72089,MA0018.2;0.665878,MA0099.2;2.31555,MA0079.2;4.97618e-06,MA0102.2;1.00004,MA0258.1;0.260331,MA0259.1;0.348068,MA0442.1;0}}
|full_id=C420_schwannoma_salivary_Mammary_skin_squamous_Smooth_cervical
|id=C420
}}

Latest revision as of 11:22, 17 September 2013


Full id: C420_schwannoma_salivary_Mammary_skin_squamous_Smooth_cervical



Phase1 CAGE Peaks

Hg19::chr10:28297133..28297154,-p@chr10:28297133..28297154
-
Hg19::chr15:40669843..40669854,-p@chr15:40669843..40669854
-
Hg19::chr17:16323425..16323480,+p@chr17:16323425..16323480
+
Hg19::chr17:65235942..65235949,-p16@HELZ
Hg19::chr18:26454397..26454408,+p@chr18:26454397..26454408
+
Hg19::chr18:26454426..26454442,+p@chr18:26454426..26454442
+
Hg19::chr1:152747609..152747621,+p@chr1:152747609..152747621
+
Hg19::chr1:152748895..152748921,+p1@LCE1F
Hg19::chr1:152758726..152758741,+p1@LCE1E
Hg19::chr20:40634129..40634138,+p@chr20:40634129..40634138
+
Hg19::chr2:153381914..153381934,+p@chr2:153381914..153381934
+
Hg19::chr2:153381962..153381984,+p@chr2:153381962..153381984
+
Hg19::chr2:153382238..153382249,+p@chr2:153382238..153382249
+
Hg19::chr3:189506429..189506448,+p@chr3:189506429..189506448
+
Hg19::chr3:6221506..6221523,-p@chr3:6221506..6221523
-
Hg19::chr3:6221525..6221536,-p@chr3:6221525..6221536
-
Hg19::chr4:177302052..177302063,+p@chr4:177302052..177302063
+
Hg19::chr4:177302106..177302128,+p@chr4:177302106..177302128
+
Hg19::chr7:15599916..15599923,-p@chr7:15599916..15599923
-
Hg19::chr8:16425118..16425128,-p12@MSR1
Hg19::chr8:36807661..36807695,-p@chr8:36807661..36807695
-
Hg19::chr8:36807702..36807719,-p@chr8:36807702..36807719
-
Hg19::chr8:36807722..36807727,-p@chr8:36807722..36807727
-
Hg19::chrY:23566622..23566663,-p@chrY:23566622..23566663
-


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:0031424keratinization0.000349270608805736
GO:0009913epidermal cell differentiation0.000349270608805736
GO:0048730epidermis morphogenesis0.000349270608805736
GO:0048729tissue morphogenesis0.000450575533477953
GO:0008544epidermis development0.0012403453005068
GO:0007398ectoderm development0.0012403453005068
GO:0009888tissue development0.00462729906663375
GO:0006898receptor-mediated endocytosis0.0409613735985991
GO:0009653anatomical structure morphogenesis0.0412754389292683
GO:0048513organ development0.0439555245850907



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
peripheral nervous system9.75e-458


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)
MA0003.13.13302e-05
MA0004.10.430931
MA0006.10.0576274
MA0007.10.801773
MA0009.10.495012
MA0014.10.00150727
MA0017.10.0747264
MA0019.11.24577
MA0024.10.404839
MA0025.10.614568
MA0027.12.05626
MA0028.10.0643724
MA0029.10.421158
MA0030.10.41146
MA0031.10.357843
MA0038.10.594428
MA0040.10.426128
MA0041.10.150655
MA0042.10.131332
MA0043.10.495289
MA0046.10.485466
MA0048.10.443269
MA0050.10.131853
MA0051.10.203156
MA0052.10.429421
MA0055.10.49738
MA0056.10
MA0057.10.0582452
MA0058.10.292964
MA0059.10.291213
MA0060.10.221405
MA0061.10.870948
MA0063.10
MA0066.10.206381
MA0067.10.78548
MA0068.10.0418736
MA0069.10.482095
MA0070.10.472333
MA0071.10.179775
MA0072.10.468422
MA0073.10.0233654
MA0074.10.202636
MA0076.10.094817
MA0077.10.461731
MA0078.10.275364
MA0081.10.6081
MA0083.10.501617
MA0084.10.964138
MA0087.10.466297
MA0088.10.499444
MA0089.10
MA0090.11.13384
MA0091.10.856604
MA0092.10.378282
MA0093.10.213685
MA0095.10
MA0098.10
MA0100.10.215803
MA0101.10.821369
MA0103.10.198896
MA0105.10.362357
MA0106.10.235406
MA0107.10.577353
MA0108.20.355343
MA0109.10
MA0111.10.109681
MA0113.10.247415
MA0114.10.306489
MA0115.10.71383
MA0116.10.588414
MA0117.10.528241
MA0119.10.569272
MA0122.11.35859
MA0124.10.675302
MA0125.11.45755
MA0130.10
MA0131.10.289284
MA0132.10
MA0133.10
MA0135.10.521813
MA0136.11.14145
MA0139.10.0119363
MA0140.10.178014
MA0141.10.0853004
MA0142.10.33212
MA0143.10.247545
MA0144.11.196
MA0145.10.00708665
MA0146.12.28252e-06
MA0147.10.330796
MA0148.10.469347
MA0149.10.17166
MA0062.20.0628366
MA0035.20.177548
MA0039.20.000705892
MA0138.20.276299
MA0002.20.642982
MA0137.20.511766
MA0104.20.0196756
MA0047.20.226642
MA0112.20.022609
MA0065.20.145654
MA0150.10.0992631
MA0151.10
MA0152.10.537486
MA0153.10.583009
MA0154.10.537265
MA0155.10.0527191
MA0156.10.885166
MA0157.10.835144
MA0158.10
MA0159.10.0358122
MA0160.10.164277
MA0161.10
MA0162.10.00132146
MA0163.10.0056464
MA0164.10.712784
MA0080.21.72089
MA0018.20.665878
MA0099.22.31555
MA0079.24.97618e-06
MA0102.21.00004
MA0258.10.260331
MA0259.10.348068
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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