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Coexpression cluster:C1479: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.555913,1.36279,0.707204,0.635275,1.56773,0.391663,0.415981,0.889639,0.336106,0.236034,0.800617,0.436569,1.53265,1.41165,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,1.04549,0.530785,0.92701,0.302275,0.640661,2.52957,0.577216,0.35388,2.44137,0.878269,0.69481,0.355745,0.513952,0.323162,0.390088,0.636689,1.18176,0.66382,0.542147,0.304272,1.02586,0.745008,2.73134,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,2.54967,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.882224,1.15727,0.218784,0.594475,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,1.37357,1.10535,0.406668,10.6033,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,1.53398,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,1.21803,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,2.40624,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,0.510514,0.306342,0.8388,0.639143,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.307168
|tfbs_overrepresentation_jaspar=MA0003.1;1.37104,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.491287,MA0017.1;0.432438,MA0019.1;1.69574,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;4.39153,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;2.74001,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;1.35477,MA0061.1;0.671725,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;1.72313,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;13.1257,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;1.37996,MA0092.1;1.29635,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;1.62836,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;1.84113,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;1.70894,MA0146.1;2.91645,MA0147.1;0.87383,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.35955,MA0138.2;1.80506,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;1.35181,MA0047.2;0.695777,MA0112.2;0.680553,MA0065.2;0.354331,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;3.55553,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.150673,MA0163.1;5.79417,MA0164.1;0.738243,MA0080.2;1.02158,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.62382,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 19:57, 22 January 2013


Full id: C1479_tonsil_Nucleus_thymus_Anulus_neuroectodermal_vein_throat



Phase1 CAGE Peaks

Hg19::chr20:21686290..21686311,+p2@PAX1
Hg19::chr20:21686317..21686350,+p1@PAX1
Hg19::chr20:21687193..21687206,+p4@PAX1
Hg19::chr20:21687260..21687270,+p3@PAX1
Hg19::chr20:21695337..21695345,+p@chr20:21695337..21695345
+
Hg19::chr20:21695435..21695452,+p@chr20:21695435..21695452
+


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
intervertebral cartilage2.85e-315
symphysis2.85e-315
nonsynovial joint2.85e-315
fibrous joint2.85e-315
cartilaginous joint2.85e-315
developing mesenchymal condensation2.85e-315
pre-cartilage condensation2.85e-315
cartilaginous condensation2.85e-315
cartilage element2.85e-315
post-cranial axial skeletal system2.85e-315
vertebral column2.85e-315
intervertebral disk2.85e-315
intervertebral joint2.85e-315
articulation1.75e-198
skeletal joint1.75e-198
articular system1.75e-198
nucleus pulposus2.55e-193
axial mesoderm2.55e-193
notochord2.55e-193
chordamesoderm2.55e-193
chordate pharynx4.05e-1510
pharyngeal region of foregut4.05e-1510
annulus fibrosus9.52e-142
fibrocartilage9.52e-142
annulus fibrosus disci intervertebralis9.52e-142
pharynx1.00e-1311
subdivision of skeletal system2.45e-1316
throat4.68e-132
neck5.43e-1010
cartilage tissue1.89e-093
skeletal tissue1.89e-093
tongue7.72e-093
gustatory system7.72e-093
future tongue7.72e-093
segment of respiratory tract8.42e-0947
pharyngeal arch system3.97e-0818
upper respiratory tract7.72e-0819
tonsil1.27e-071
mucosa-associated lymphoid tissue1.27e-071
lymphoid tissue1.27e-071
tonsillar ring1.27e-071
respiratory tract1.80e-0754
surface2.37e-071
thymus3.74e-074
hemolymphoid system gland3.74e-074
thymic region3.74e-074
pharyngeal gland3.74e-074
thymus primordium3.74e-074
axial skeletal system4.38e-0714


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)
MA0003.11.37104
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
MA0017.10.432438
MA0019.11.69574
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.14.39153
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.12.74001
MA0058.10.458909
MA0059.10.457555
MA0060.11.35477
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.72313
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.113.1257
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.11.29635
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.11.62836
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.70894
MA0146.12.91645
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.35955
MA0138.21.80506
MA0002.20.255126
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.680553
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.13.55553
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.15.79417
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.20.62382
MA0102.21.58513
MA0258.10.788656
MA0259.10.893594
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
SUZ12#23512433.41052060737532.29902183370319e-068.1920007263776e-05



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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