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Coexpression cluster:C944: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.312007,0.00986147,0.305225,0.440628,0.267236,1.11855,0.511871,0.164003,0.161941,0.0287394,0.410439,0.553754,0.127813,0.500805,0.266007,0.782718,0.728104,0.218596,0.137566,0.818932,0.305279,0.0355541,0.431698,0.262652,0.918075,0.575764,3.80724,0.429643,0.270022,0.676,0.389837,0.764231,0.190489,0.807612,0.23642,0.045176,0.233607,0.440165,1.14973,0.14756,0.663028,0.374544,0.366128,0.731232,0.0112275,0.333541,0.51292,0.4002,0.0372068,0.743836,0.589559,0.524278,0.0739421,0.839846,0.99088,0.503626,0.273964,0.472204,0.329728,0.47124,0.804523,0.5152,0.488493,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.504216,0.0724994,0.988898,0.124338,0.114787,0.105027,0.684401,0.750836,0.341765,1.38495,0.699894,4.4988,0.498312,0.937974,0.0150019,0.0591186,0.096982,0.614883,1.54397,2.63353,0.911274,0.78075,0.571859,0.267904,0.207949,0.837326,0.82268,0.619373,0.0858425,0.613956,1.82563,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,0.814459,0.300169,0.41935,1.12352,0.232218,0.0194997,0.388709,0.664981,0.577715,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,1.79896,1.03718,0.539846,1.18405,0.0922077,2.65836,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,3.8858,0.464114,0.641461,1.83907,0.37143,0.193834,0.0656964,0.0382049,0.912334,0.155464,1.28086,8.61216,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,1.55897,0.673453,3.33235,0.183544,0.510589,0.00185481
|tfbs_overrepresentation_jaspar=MA0003.1;0.000472949,MA0004.1;0.415381,MA0006.1;0.265592,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.00594475,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;0.280275,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;1.28049,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;0.0764047,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;3.10954,MA0055.1;0.0199484,MA0056.1;0,MA0057.1;0.0725989,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;0.162248,MA0061.1;0.139804,MA0063.1;0,MA0066.1;2.21042,MA0067.1;1.18766,MA0068.1;0.109867,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;3.19635e-05,MA0074.1;0.509711,MA0076.1;0.339975,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;0.0408613,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.271368,MA0103.1;0.257174,MA0105.1;0.0643619,MA0106.1;0.554855,MA0107.1;0.205358,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;0.200901,MA0115.1;1.11137,MA0116.1;0.208403,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;0.474342,MA0141.1;0.322254,MA0142.1;3.97811,MA0143.1;3.50824,MA0144.1;0.1885,MA0145.1;0.046841,MA0146.1;0.0045741,MA0147.1;0.211483,MA0148.1;1.11902,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;0.0006485,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.28622,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;0.0433683,MA0065.2;0.0483532,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.062786,MA0155.1;0.0402662,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.0107891,MA0163.1;0.00648562,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;2.18822e-08,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.218904,MA0442.1;0
}}
}}

Revision as of 19:34, 22 January 2013


Full id: C944_adipose_lung_cervix_epididymis_testis_aorta_breast



Phase1 CAGE Peaks

Hg19::chr3:155860767..155860786,+p3@KCNAB1
Hg19::chr4:143227063..143227074,-p9@INPP4B
Hg19::chr4:143227088..143227105,-p6@INPP4B
Hg19::chr6:97010976..97010989,+p5@FHL5
Hg19::chr6:97010993..97011021,+p1@FHL5
Hg19::chr6:97011046..97011069,+p2@FHL5
Hg19::chr6:97011080..97011094,+p4@FHL5
Hg19::chr6:97011096..97011111,+p6@FHL5
Hg19::chr6:97011128..97011135,+p8@FHL5


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:0016316phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity0.0109498719381662
GO:0042577lipid phosphatase activity0.0328341461007309
GO:0015459potassium channel regulator activity0.0328341461007309
GO:0016247channel regulator activity0.0492251227199647



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
adult organism2.80e-99114
neural tube1.35e-2656
neural rod1.35e-2656
future spinal cord1.35e-2656
neural keel1.35e-2656
regional part of nervous system6.29e-2353
regional part of brain6.29e-2353
neural plate1.27e-2082
presumptive neural plate1.27e-2082
central nervous system2.68e-1981
neurectoderm3.52e-1986
regional part of forebrain4.13e-1841
forebrain4.13e-1841
anterior neural tube4.13e-1841
future forebrain4.13e-1841
structure with developmental contribution from neural crest2.02e-17132
brain5.25e-1768
future brain5.25e-1768
nervous system2.10e-1689
telencephalon1.25e-1534
organ system subdivision1.43e-15223
brain grey matter2.29e-1534
gray matter2.29e-1534
ecto-epithelium4.13e-14104
cerebral hemisphere1.80e-1332
regional part of telencephalon2.00e-1332
anatomical cluster3.21e-13373
multi-tissue structure2.81e-12342
pre-chordal neural plate2.93e-1161
anatomical conduit2.97e-11240
regional part of cerebral cortex3.89e-1122
neocortex1.27e-1020
ectoderm-derived structure3.12e-10171
ectoderm3.12e-10171
presumptive ectoderm3.12e-10171
posterior neural tube8.89e-1015
chordal neural plate8.89e-1015
cerebral cortex1.78e-0925
pallium1.78e-0925
tube4.62e-09192
organ4.96e-09503
neural nucleus6.17e-089
nucleus of brain6.17e-089
male genital duct1.92e-073
internal male genitalia1.92e-073
compound organ3.19e-0768
multi-cellular organism3.50e-07656
cardiac chamber5.07e-073
brainstem5.58e-076
valve5.60e-073
cardiac mesenchyme5.60e-073
cardial valve5.60e-073
tunica intima5.60e-073
heart layer5.60e-073
endocardium5.60e-073
endocardial cushion5.60e-073
presumptive endocardium5.60e-073
embryo9.09e-07592
organ part9.75e-07218


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)
MA0003.10.000472949
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.11.28049
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.13.10954
MA0055.10.0199484
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.12.21042
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.13.97811
MA0143.13.50824
MA0144.10.1885
MA0145.10.046841
MA0146.10.0045741
MA0147.10.211483
MA0148.11.11902
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.0402662
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.22.18822e-08
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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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