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Coexpression cluster:C2849: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,0.151681,0.706765,0.867962,0.341754,0.809319,2.26901,1.37557,1.05593,0.471262,0.938585,0.635753,1.42279,0.975621,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,1.63146,0.53106,0.314427,0.61613,0.822818,0.694903,0.99221,2.28614,0.90714,0.83543,0.699149,1.17354,1.33024,1.90242,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,1.80204,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.823598,1.00941,1.08,2.5716,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,2.2083,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,2.0177,0.354969,1.15558,0.939507,0.272395,2.04634,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,1.11576,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,1.28873,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.00378
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,0.151681,0.706765,0.867962,0.341754,0.809319,2.26901,1.37557,1.05593,0.471262,0.938585,0.635753,1.42279,0.975621,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,1.63146,0.53106,0.314427,0.61613,0.822818,0.694903,0.99221,2.28614,0.90714,0.83543,0.699149,1.17354,1.33024,1.90242,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,1.80204,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.823598,1.00941,1.08,2.5716,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,2.2083,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,2.0177,0.354969,1.15558,0.939507,0.272395,2.04634,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,1.11576,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,1.28873,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.00378
|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;1.66514,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;1.66718,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;1.8408,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;1.91637,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;4.39922,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;1.70187,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;1.29536,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;1.46638,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;1.37305,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;2.98688,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:57, 22 January 2013


Full id: C2849_Mast_plasma_splenic_migratory_Burkitt_CD14CD16_xeroderma



Phase1 CAGE Peaks

Hg19::chr6:155504411..155504418,+p16@TIAM2
Hg19::chr6:155504423..155504442,+p4@TIAM2
Hg19::chr6:155504446..155504462,+p5@TIAM2
Hg19::chr6:155504495..155504502,+p@chr6:155504495..155504502
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
leukocyte1.04e-65136
nongranular leukocyte7.28e-54115
hematopoietic lineage restricted progenitor cell1.62e-53120
hematopoietic cell1.33e-51177
hematopoietic stem cell1.40e-49168
angioblastic mesenchymal cell1.40e-49168
hematopoietic oligopotent progenitor cell3.54e-49161
hematopoietic multipotent progenitor cell3.54e-49161
myeloid leukocyte1.91e-4572
classical monocyte1.87e-4442
CD14-positive, CD16-negative classical monocyte1.87e-4442
defensive cell9.06e-4348
phagocyte9.06e-4348
granulocyte monocyte progenitor cell1.11e-3967
macrophage dendritic cell progenitor3.24e-3961
monopoietic cell1.17e-3859
monocyte1.17e-3859
monoblast1.17e-3859
promonocyte1.17e-3859
myeloid lineage restricted progenitor cell2.51e-3866
myeloid cell7.56e-33108
common myeloid progenitor7.56e-33108
lymphocyte of B lineage3.26e-3224
pro-B cell3.26e-3224
B cell1.67e-2014
stuff accumulating cell4.64e-1987
lymphoid lineage restricted progenitor cell1.30e-1452
mesenchymal cell2.20e-14354
lymphocyte3.20e-1453
common lymphoid progenitor3.20e-1453
connective tissue cell9.41e-14361
nucleate cell1.76e-1355
intermediate monocyte7.17e-129
CD14-positive, CD16-positive monocyte7.17e-129
motile cell1.51e-11386
conventional dendritic cell5.26e-118
circulating cell3.33e-096
multi fate stem cell6.77e-09427
dendritic cell8.69e-0910
stem cell1.40e-08441
somatic stem cell1.55e-08433
non-classical monocyte2.90e-083
CD14-low, CD16-positive monocyte2.90e-083
Langerhans cell9.01e-085
basophil3.99e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.35e-4698
blood island1.35e-4698
hemolymphoid system8.52e-43108
immune system3.02e-3593
bone marrow1.24e-3376
bone element5.13e-3282
skeletal element3.84e-2890
skeletal system3.53e-24100
lateral plate mesoderm1.01e-16203
connective tissue6.77e-13371
musculoskeletal system1.15e-11167
mesoderm4.04e-09315
mesoderm-derived structure4.04e-09315
presumptive mesoderm4.04e-09315
blood4.47e-0815
haemolymphatic fluid4.47e-0815
organism substance4.47e-0815
spleen8.83e-073
gastrointestinal system mesentery8.83e-073
stomach region8.83e-073
mesentery8.83e-073
gastrointestinal system serosa8.83e-073
mesentery of stomach8.83e-073
gut mesentery8.83e-073
dorsal mesentery8.83e-073
dorsal mesogastrium8.83e-073
peritoneal cavity8.83e-073
spleen primordium8.83e-073
hemopoietic organ9.39e-077
immune organ9.39e-077
Disease
Ontology termp-valuen
lymphoma2.68e-0710


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.11.66514
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.11.8408
MA0072.11.1744
MA0073.10.00636811
MA0074.11.91637
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.14.39922
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.11.70187
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.12.98688
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
TAF1#687243.343046285745290.008005664898701650.0323231776532069
YY1#752844.911170749853860.00171871838055440.0107037107302756



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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