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Coexpression cluster:C1481: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.603698,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.075749,1.36279,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.800617,0.436569,0.6169,0.576478,0.387783,0.483957,0.730467,1.10781,2.40434,0.396295,2.34526,0.530785,0.92701,0.302275,0.640661,1.67655,0.909936,0.35388,2.44137,0.329602,1.9886,0.355745,1.2792,0.323162,0.390088,0.0393783,0.468392,1.59472,0.542147,0.304272,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,3.72327,0.186533,0.619193,0.968558,2.7005,0.267534,0.861462,2.75922,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.882224,1.15727,0.218784,0.594475,1.68655,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.181326,0.398737,0.181871,1.81827,1.71797,1.34233,1.07807,0.94406,0.30974,5.90291,0.32338,1.91313,0.987239,1.82799,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,3.11809,0.376529,0.44815,0.978783,2.87604,0.563054,1.29401,2.50577,1.70375,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,1.06652,1.07915,1.32317,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,1.45122,0.661335,1.11626
|tfbs_overrepresentation_jaspar=MA0003.1;0.176622,MA0004.1;5.91984,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.491287,MA0017.1;0.432438,MA0019.1;0.7124,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;1.45353,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.213007,MA0056.1;0,MA0057.1;0.450439,MA0058.1;2.02413,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;1.59928,MA0067.1;1.35893,MA0068.1;1.09642,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.959858,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;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;4.77106,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.419295,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;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.641617,MA0140.1;3.73326,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.093337,MA0147.1;3.2919,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.0929059,MA0138.2;0.765223,MA0002.2;0.709311,MA0137.2;0.414885,MA0104.2;2.90014,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.65596,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.347838,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.476723,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;5.40068,MA0442.1;0
}}
}}

Revision as of 19:57, 22 January 2013


Full id: C1481_CD4_CD8_thymus_CD14CD16_CD14_granulocyte_CD19



Phase1 CAGE Peaks

Hg19::chr20:52226313..52226350,-p3@ZNF217
Hg19::chr2:182322070..182322155,+p1@ITGA4
Hg19::chr2:182322911..182322927,+p12@ITGA4
Hg19::chr2:182322938..182322962,+p5@ITGA4
Hg19::chr2:182322965..182322977,+p13@ITGA4
Hg19::chr2:182322985..182322998,+p10@ITGA4


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
hematopoietic stem cell1.12e-79168
angioblastic mesenchymal cell1.12e-79168
hematopoietic cell9.62e-76177
hematopoietic oligopotent progenitor cell1.02e-73161
hematopoietic multipotent progenitor cell1.02e-73161
leukocyte1.35e-62136
hematopoietic lineage restricted progenitor cell4.63e-56120
nongranular leukocyte5.41e-55115
myeloid cell6.02e-38108
common myeloid progenitor6.02e-38108
nucleate cell1.43e-3355
lymphocyte2.33e-3253
common lymphoid progenitor2.33e-3253
lymphoid lineage restricted progenitor cell6.79e-3252
mesenchymal cell2.74e-26354
connective tissue cell1.33e-25361
myeloid lineage restricted progenitor cell4.84e-2366
granulocyte monocyte progenitor cell6.85e-2367
myeloid leukocyte1.08e-2272
motile cell5.82e-21386
macrophage dendritic cell progenitor1.86e-2061
monopoietic cell4.40e-2059
monocyte4.40e-2059
monoblast4.40e-2059
promonocyte4.40e-2059
classical monocyte1.16e-1942
CD14-positive, CD16-negative classical monocyte1.16e-1942
defensive cell6.91e-1848
phagocyte6.91e-1848
multi fate stem cell5.90e-17427
T cell1.73e-1625
pro-T cell1.73e-1625
stem cell2.13e-16441
mature alpha-beta T cell5.80e-1618
alpha-beta T cell5.80e-1618
immature T cell5.80e-1618
mature T cell5.80e-1618
immature alpha-beta T cell5.80e-1618
somatic stem cell6.23e-16433
lymphocyte of B lineage5.78e-1424
pro-B cell5.78e-1424
CD8-positive, alpha-beta T cell2.75e-1111
B cell4.17e-1114
intermediate monocyte1.34e-079
CD14-positive, CD16-positive monocyte1.34e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.92e-3398
blood island3.92e-3398
hemolymphoid system2.95e-29108
connective tissue7.90e-24371
immune system9.44e-2193
bone marrow9.38e-2076
bone element1.26e-1982
skeletal element3.12e-1790
skeletal system5.95e-15100
blood1.41e-1015
haemolymphatic fluid1.41e-1015
organism substance1.41e-1015
lateral plate mesoderm8.96e-07203
Disease
Ontology termp-valuen
hematologic cancer3.58e-1751
immune system cancer3.58e-1751
leukemia8.87e-1539
myeloid leukemia1.05e-1231


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)
MA0003.10.176622
MA0004.15.91984
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
MA0017.10.432438
MA0019.10.7124
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
MA0048.11.45353
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.450439
MA0058.12.02413
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.11.59928
MA0067.11.35893
MA0068.11.09642
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.959858
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.14.77106
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
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
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.13.73326
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.093337
MA0147.13.2919
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0929059
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.22.90014
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.476723
MA0102.21.58513
MA0258.10.289793
MA0259.15.40068
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
CTCF#1066454.466880310895860.001144848346172360.00783633611390057
EBF1#187945.937644564379340.001975153636421710.0114914528791848
EGR1#195854.156815912341780.001617966818864440.0101348789417251
GATA1#2623511.30025678650041.22736455569136e-050.000305274414936533
MAX#414955.377129590839270.000467001558889580.0042949256612248
MYC#460965.22228187160944.92821127172503e-050.000854269638187039
NFKB1#479054.57338618682820.00102196259371130.00724692771079672
POLR2A#543062.147453176558070.01019570676818780.038048646436174
SIN3A#2594243.605923151210090.01273893844487140.0459454360687889
TAF1#687252.785871904787740.01078636340290410.0397978169800006
USF1#739144.240999518138640.007005367750829420.0296088062536978
YY1#752854.092642291544880.001743365462849530.0107267200173525



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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