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Coexpression cluster:C1556: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.26722,0.787587,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,0.345702,2.55627,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,1.42981,1.54297,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,1.16016,0.233785,0.598009,1.00172,0.94379,0.758594,1.88355,0.432883,1.06371,1.57519,0.388123,2.25858,0.415749,1.42042,0.132849,0.451846,1.74542,1.32072,0.734485,0.609718,0.393318,0.458489,1.91222,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,1.74665,0.321912,0.935408,1.78554,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,2.36503,1.23387,2.91664,1.30959,0.240727,0.917983,0.987729,0.543014,0.293154,2.1521,0.755403,0.327263,1.18161,1.89992,0.49825,2.64291,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,2.6759,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,1.8413,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.526389,0.79475,1.15522,1.51895,0.736459,1.56426,0.827475,0.439798,0.54968,2.22269,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,2.39025
|tfbs_overrepresentation_for_novel_motifs=1.26722,0.787587,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,0.345702,2.55627,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,1.42981,1.54297,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,1.16016,0.233785,0.598009,1.00172,0.94379,0.758594,1.88355,0.432883,1.06371,1.57519,0.388123,2.25858,0.415749,1.42042,0.132849,0.451846,1.74542,1.32072,0.734485,0.609718,0.393318,0.458489,1.91222,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,1.74665,0.321912,0.935408,1.78554,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,2.36503,1.23387,2.91664,1.30959,0.240727,0.917983,0.987729,0.543014,0.293154,2.1521,0.755403,0.327263,1.18161,1.89992,0.49825,2.64291,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,2.6759,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,1.8413,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.526389,0.79475,1.15522,1.51895,0.736459,1.56426,0.827475,0.439798,0.54968,2.22269,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,2.39025
|tfbs_overrepresentation_jaspar=MA0003.1;2.24383,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;2.48957,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;2.33564,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;1.01397,MA0056.1;0,MA0057.1;2.36624,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.215829,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;1.3271,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.520776,MA0106.1;1.83541,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;2.70679,MA0146.1;0.6031,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;3.99004,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;1.12758,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.839774,MA0065.2;0.880827,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.813062,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;1.00463,MA0160.1;0.669748,MA0161.1;0,MA0162.1;2.88007,MA0163.1;1.99104,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;13.6951,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:01, 22 January 2013


Full id: C1556_epididymis_seminal_Renal_ductus_kidney_rhabdomyosarcoma_renal



Phase1 CAGE Peaks

Hg19::chr10:102505147..102505162,+p9@PAX2
Hg19::chr10:102505297..102505302,+p11@PAX2
Hg19::chr10:102505493..102505546,+p2@PAX2
Hg19::chr10:102505946..102505949,+p14@PAX2
Hg19::chr10:102505954..102505973,+p3@PAX2


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

No GOStat results

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
kidney5.34e-4726
kidney mesenchyme5.34e-4726
upper urinary tract5.34e-4726
kidney rudiment5.34e-4726
kidney field5.34e-4726
cavitated compound organ5.86e-4431
nephron tubule epithelium2.65e-3110
excretory tube4.58e-3016
kidney epithelium4.58e-3016
urinary system structure1.68e-2747
renal system7.61e-2748
nephron epithelium6.77e-2615
renal tubule6.77e-2615
nephron tubule6.77e-2615
nephron6.77e-2615
uriniferous tubule6.77e-2615
nephrogenic mesenchyme6.77e-2615
abdomen element1.83e-2354
abdominal segment element1.83e-2354
abdominal segment of trunk1.00e-2060
abdomen1.00e-2060
cortex2.84e-2015
cortex of kidney7.09e-2012
renal parenchyma7.09e-2012
compound organ6.82e-1868
male genital duct1.01e-163
internal male genitalia1.01e-163
parenchyma1.03e-1515
posterior neural tube5.82e-1515
chordal neural plate5.82e-1515
mesonephros1.87e-149
pronephros1.87e-149
nephrogenic cord1.87e-149
pronephric mesoderm1.87e-149
rostral part of nephrogenic cord1.87e-149
presumptive pronephric mesoderm1.87e-149
segmental subdivision of hindbrain6.12e-1412
hindbrain6.12e-1412
presumptive hindbrain6.12e-1412
brainstem4.53e-136
segmental subdivision of nervous system7.97e-1313
duct of male reproductive system1.16e-124
trunk region element3.21e-12101
urogenital ridge8.97e-1211
abdomen connective tissue1.72e-112
abdominal segment connective tissue1.72e-112
trunk connective tissue1.72e-112
interstitial tissue1.72e-112
extraglomerular mesangium1.72e-112
kidney interstitium1.72e-112
juxtaglomerular apparatus1.72e-112
mesangium1.72e-112
intraembryonic coelom9.12e-1112
mesonephric epithelium1.10e-108
mesonephric tubule1.10e-108
nephric duct1.10e-108
renal duct1.10e-108
mesonephric duct1.10e-108
pronephric duct1.10e-108
locus ceruleus1.42e-102
brainstem nucleus1.42e-102
hindbrain nucleus1.42e-102
adult organism9.07e-10114
duct2.05e-0919
subdivision of trunk2.49e-09112
regional part of metencephalon9.82e-099
metencephalon9.82e-099
future metencephalon9.82e-099
intermediate mesoderm5.38e-0828
male reproductive organ1.17e-0711
renal cortex tubule1.26e-073
region of nephron tubule1.26e-073
proximal tubule1.26e-073
medulla oblongata2.13e-073
myelencephalon2.13e-073
future myelencephalon2.13e-073
pons2.50e-073
primitive nephron3.26e-077
renal glomerulus3.26e-077
renal corpuscle3.26e-077
glomerular capsule3.26e-077
metanephric mesenchyme3.26e-077
glomerular tuft3.26e-077


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)
MA0003.12.24383
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.12.48957
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.12.33564
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.12.36624
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.11.83541
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.12.70679
MA0146.10.6031
MA0147.10.386018
MA0148.10.653474
MA0149.13.99004
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.12.88007
MA0163.11.99104
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.213.6951
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CTBP2#1488337.63020020359693.95343056005017e-050.000737439425363601
SUZ12#23512220.04631236442520.003824075654154750.0188717401712549



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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