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Coexpression cluster:C477: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.111472,0.638902,0.348202,0.19904,0.601808,0.574869,1.30167,0.58907,0.914779,0.567121,0.177199,1.4241,1.89531,0.244498,0.598404,0.65729,0.43322,0.214415,0.775214,1.04122,0.107335,0.678538,0.192508,0.0823774,0.134089,0.304148,0.627278,0.191013,2.08386,0.559665,0.489389,0.465029,0.174335,0.2371,1.84983,0.117893,0.509344,0.1987,0.206488,0.282055,0.0675531,0.904491,1.34075,0.283867,1.14645,0.125045,0.706544,0.507207,0.318317,0.609855,0.315441,0.727101,0.229319,0.532773,0.671855,0.246686,0.298409,0.222594,0.55919,0.221865,0.500944,0.255713,0.582321,0.409576,0.269358,0.380605,0.754286,1.10771,0.456006,0.950487,0.442439,0.608338,0.00682481,0.670004,0.224282,0.390082,0.351133,0.395294,0.45319,0.130356,0.109737,0.408665,0.269087,0.141606,0.622646,0.646717,0.173153,0.0595657,0.336397,1.20481,0.84263,0.598,0.4797,0.182928,0.288936,0.0539379,0.25404,0.517267,0.340143,0.727664,0.0570156,0.474756,0.512318,0.436368,0.371019,0.174162,1.08332,0.241933,0.133935,0.265841,0.364924,0.509866,0.34005,0.540387,0.797061,0.505559,1.02351,0.487455,0.378653,0.186375,0.662347,0.334429,0.195973,0.277756,0.90249,0.395934,0.248345,2.10815,0.701879,1.65396,0.598629,0.494009,0.715286,0.275188,0.854902,0.30041,0.479764,1.67801,0.814541,1.65405,1.25623,0.779227,0.249639,0.514137,0.372477,0.619113,0.35869,1.49614,0.150069,0.402254,0.818697,0.0117055,0.598976,0.127482,0.255347,0.980005,0.32333,0.268575,0.134125,0.116987,0.77808,0.582159,0.452507,0.760235,0.385896,0.268483,0.16475,0.702336,3.10016
|tfbs_overrepresentation_jaspar=MA0003.1;4.30904,MA0004.1;0.180726,MA0006.1;0.0840255,MA0007.1;0.970384,MA0009.1;0.561062,MA0014.1;0.211507,MA0017.1;0.342408,MA0019.1;0.290278,MA0024.1;0.467291,MA0025.1;0.684106,MA0027.1;2.13512,MA0028.1;0.308337,MA0029.1;0.484339,MA0030.1;0.474212,MA0031.1;0.41796,MA0038.1;0.25521,MA0040.1;0.489524,MA0041.1;0.193578,MA0042.1;0.171628,MA0043.1;0.561349,MA0046.1;0.551181,MA0048.1;0.113667,MA0050.1;0.172223,MA0051.1;0.251994,MA0052.1;0.492957,MA0055.1;0.589179,MA0056.1;0,MA0057.1;0.893467,MA0058.1;0.119655,MA0059.1;0.760411,MA0060.1;0.0338613,MA0061.1;0.0254296,MA0063.1;0,MA0066.1;0.255535,MA0067.1;0.858361,MA0068.1;0.614744,MA0069.1;0.547689,MA0070.1;0.537571,MA0071.1;0.22617,MA0072.1;0.533514,MA0073.1;0.42958,MA0074.1;0.251422,MA0076.1;1.30941,MA0077.1;0.526569,MA0078.1;0.33032,MA0081.1;0.76084,MA0083.1;0.567893,MA0084.1;1.03923,MA0087.1;0.531309,MA0088.1;0.207879,MA0089.1;0,MA0090.1;0.138104,MA0091.1;1.02897,MA0092.1;0.157193,MA0093.1;0.0855877,MA0095.1;0,MA0098.1;0,MA0100.1;0.265855,MA0101.1;0.0872967,MA0103.1;0.27232,MA0105.1;1.44333,MA0106.1;0.28721,MA0107.1;0.0527035,MA0108.2;0.415325,MA0109.1;0,MA0111.1;0.449411,MA0113.1;0.812272,MA0114.1;0.188951,MA0115.1;0.785493,MA0116.1;1.65131,MA0117.1;0.595385,MA0119.1;1.18223,MA0122.1;0.619196,MA0124.1;0.746208,MA0125.1;0.667416,MA0130.1;0,MA0131.1;0.345226,MA0132.1;0,MA0133.1;0,MA0135.1;0.588754,MA0136.1;0.260607,MA0139.1;0.237867,MA0140.1;0.224213,MA0141.1;0.117869,MA0142.1;0.39079,MA0143.1;0.300362,MA0144.1;0.388125,MA0145.1;1.1391,MA0146.1;1.5232,MA0147.1;0.783008,MA0148.1;0.575245,MA0149.1;0.21714,MA0062.2;0.102633,MA0035.2;0.223695,MA0039.2;2.99103,MA0138.2;1.5856,MA0002.2;0.542267,MA0137.2;0.317751,MA0104.2;0.912884,MA0047.2;0.761085,MA0112.2;0.372295,MA0065.2;0.415474,MA0150.1;0.134443,MA0151.1;0,MA0152.1;0.229055,MA0153.1;0.65174,MA0154.1;3.13195,MA0155.1;1.31756,MA0156.1;0.0971366,MA0157.1;0.367703,MA0158.1;0,MA0159.1;0.785302,MA0160.1;0.20889,MA0161.1;0,MA0162.1;0.355774,MA0163.1;2.43533,MA0164.1;0.310173,MA0080.2;0.0856322,MA0018.2;0.288301,MA0099.2;0.229319,MA0079.2;3.40943,MA0102.2;1.07547,MA0258.1;0.160304,MA0259.1;0.214864,MA0442.1;0
}}
}}

Revision as of 19:12, 22 January 2013


Full id: C477_Mesenchymal_Amniotic_Placental_chorionic_umbilical_Cardiac_acute



Phase1 CAGE Peaks

Hg19::chr11:1480395..1480413,+p@chr11:1480395..1480413
+
Hg19::chr11:1897722..1897737,+p18@LSP1
Hg19::chr12:123465379..123465397,+p7@ARL6IP4
Hg19::chr14:52781196..52781213,+p3@PTGER2
Hg19::chr16:49698228..49698243,-p2@ZNF423
Hg19::chr16:89686991..89687015,+p5@DPEP1
Hg19::chr16:89687026..89687041,+p7@DPEP1
Hg19::chr17:37824505..37824516,+p11@PNMT
Hg19::chr17:37824531..37824553,+p6@PNMT
Hg19::chr17:37824598..37824605,+p15@PNMT
Hg19::chr17:37824700..37824714,+p2@PNMT
Hg19::chr17:37825180..37825196,+p@chr17:37825180..37825196
+
Hg19::chr17:7836505..7836526,+p3@CNTROB
Hg19::chr18:71928422..71928428,-p3@CYB5A
Hg19::chr1:1567682..1567692,+p1@MMP23A
Hg19::chr3:154801312..154801336,+p29@MME
Hg19::chr3:162256416..162256425,-p@chr3:162256416..162256425
-
Hg19::chr4:1166954..1166973,-p13@SPON2
Hg19::chr7:101556503..101556516,+p12@CUX1
Hg19::chr7:95979117..95979120,+p@chr7:95979117..95979120
+


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:0004603phenylethanolamine N-methyltransferase activity0.0459019238428391
GO:0007099centriole replication0.0459019238428391
GO:0051299centrosome separation0.0459019238428391
GO:0005792microsome0.0459019238428391
GO:0042598vesicular fraction0.0459019238428391
GO:0004237membrane dipeptidase activity0.0459019238428391
GO:0016564transcription repressor activity0.0466288745382801
GO:0005814centriole0.0466288745382801
GO:0051298centrosome duplication0.0466288745382801
GO:0004960thromboxane receptor activity0.0466288745382801
GO:0042423catecholamine biosynthetic process0.0466288745382801
GO:0016481negative regulation of transcription0.0466288745382801
GO:0016805dipeptidase activity0.0466288745382801
GO:0042491auditory receptor cell differentiation0.0466288745382801
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0466288745382801
GO:0007098centrosome cycle0.0466288745382801
GO:0004245neprilysin activity0.0466288745382801
GO:0042490mechanoreceptor differentiation0.0466288745382801
GO:0060113inner ear receptor cell differentiation0.0466288745382801
GO:0004957prostaglandin E receptor activity0.0466288745382801
GO:0008237metallopeptidase activity0.0466288745382801
GO:0051297centrosome organization and biogenesis0.0466288745382801
GO:0031023microtubule organizing center organization and biogenesis0.0466288745382801
GO:0031324negative regulation of cellular metabolic process0.0466288745382801
GO:0006928cell motility0.0466288745382801
GO:0051674localization of cell0.0466288745382801
GO:0008239dipeptidyl-peptidase activity0.0466288745382801
GO:0016806dipeptidyl-peptidase and tripeptidyl-peptidase activity0.0466288745382801



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
mesenchyme of umbilical cord1.61e-096


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)
MA0003.14.30904
MA0004.10.180726
MA0006.10.0840255
MA0007.10.970384
MA0009.10.561062
MA0014.10.211507
MA0017.10.342408
MA0019.10.290278
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.308337
MA0029.10.484339
MA0030.10.474212
MA0031.10.41796
MA0038.10.25521
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.10.561349
MA0046.10.551181
MA0048.10.113667
MA0050.10.172223
MA0051.10.251994
MA0052.10.492957
MA0055.10.589179
MA0056.10
MA0057.10.893467
MA0058.10.119655
MA0059.10.760411
MA0060.10.0338613
MA0061.10.0254296
MA0063.10
MA0066.10.255535
MA0067.10.858361
MA0068.10.614744
MA0069.10.547689
MA0070.10.537571
MA0071.10.22617
MA0072.10.533514
MA0073.10.42958
MA0074.10.251422
MA0076.11.30941
MA0077.10.526569
MA0078.10.33032
MA0081.10.76084
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.10.207879
MA0089.10
MA0090.10.138104
MA0091.11.02897
MA0092.10.157193
MA0093.10.0855877
MA0095.10
MA0098.10
MA0100.10.265855
MA0101.10.0872967
MA0103.10.27232
MA0105.11.44333
MA0106.10.28721
MA0107.10.0527035
MA0108.20.415325
MA0109.10
MA0111.10.449411
MA0113.10.812272
MA0114.10.188951
MA0115.10.785493
MA0116.11.65131
MA0117.10.595385
MA0119.11.18223
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.345226
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.237867
MA0140.10.224213
MA0141.10.117869
MA0142.10.39079
MA0143.10.300362
MA0144.10.388125
MA0145.11.1391
MA0146.11.5232
MA0147.10.783008
MA0148.10.575245
MA0149.10.21714
MA0062.20.102633
MA0035.20.223695
MA0039.22.99103
MA0138.21.5856
MA0002.20.542267
MA0137.20.317751
MA0104.20.912884
MA0047.20.761085
MA0112.20.372295
MA0065.20.415474
MA0150.10.134443
MA0151.10
MA0152.10.229055
MA0153.10.65174
MA0154.13.13195
MA0155.11.31756
MA0156.10.0971366
MA0157.10.367703
MA0158.10
MA0159.10.785302
MA0160.10.20889
MA0161.10
MA0162.10.355774
MA0163.12.43533
MA0164.10.310173
MA0080.20.0856322
MA0018.20.288301
MA0099.20.229319
MA0079.23.40943
MA0102.21.07547
MA0258.10.160304
MA0259.10.214864
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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