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Coexpression cluster:C890: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.83884,0.735382,0.305225,0.440628,0.267236,0.439064,0.511871,0.164003,0.94513,0.285547,0.410439,0.553754,0.40163,0.500805,0.266007,0.287179,0.728104,0.218596,0.842338,0.216842,0.305279,0.33045,1.9325,0.262652,0.347482,0.575764,0.112018,0.429643,0.74357,0.10044,0.389837,0.764231,1.06082,0.406122,0.665895,0.261421,1.90822,1.12093,0.611187,0.14756,0.235191,0.97787,0.366128,0.264644,0.0550925,0.333541,0.51292,0.4002,0.340916,0.270138,0.589559,0.524278,0.257164,0.839846,0.99088,1.25719,0.273964,0.472204,0.329728,1.18788,0.804523,0.5152,0.162346,0.700946,1.31866,0.667267,1.07848,1.44489,1.78193,1.28328,0.362234,0.168734,0.53933,0.988898,0.784625,0.114787,0.342172,0.684401,0.750836,0.905375,0.436045,0.699894,0.532172,0.498312,0.937974,1.6482,0.468577,0.320664,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.738715,0.598862,0.136404,0.82268,1.50181,0.606171,0.214313,1.82563,0.817185,0.731699,0.656016,1.04711,0.716172,1.24409,0.917554,2.00997,0.315525,0.814459,0.300169,0.41935,1.12352,0.232218,0.685543,1.78582,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,1.01734,1.03718,0.539846,1.18405,0.636999,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.565137,0.50389,1.87005,0.912334,0.918218,0.514733,1.31376,0.599133,4.6407,0.347536,0.320853,1.10357,2.06978,0.750062,0.323817,0.673453,0.531409,0.540317,0.510589,0.51231
|tfbs_overrepresentation_jaspar=MA0003.1;2.34025,MA0004.1;0.415381,MA0006.1;5.76038,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.841704,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;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;1.03929,MA0043.1;2.02319,MA0046.1;0.860127,MA0048.1;3.21312,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;0.22215,MA0056.1;0,MA0057.1;0.539841,MA0058.1;0.325084,MA0059.1;0.865474,MA0060.1;0.162248,MA0061.1;0.139804,MA0063.1;0,MA0066.1;0.514973,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;0.0176541,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;0.158781,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;0.714036,MA0105.1;0.854766,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;0.582067,MA0115.1;1.11137,MA0116.1;1.13131,MA0117.1;2.09924,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;5.77823,MA0140.1;0.474342,MA0141.1;0.322254,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.552298,MA0145.1;0.39929,MA0146.1;2.57433,MA0147.1;2.52411,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.421263,MA0035.2;0.473658,MA0039.2;1.17223,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.780538,MA0104.2;2.15714,MA0047.2;0.542971,MA0112.2;0.674448,MA0065.2;0.408099,MA0150.1;5.50349,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.842081,MA0155.1;1.00468,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.60858,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.767014,MA0163.1;1.18882,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;1.36887,MA0099.2;0.481058,MA0079.2;0.893499,MA0102.2;1.41188,MA0258.1;0.532421,MA0259.1;0.624802,MA0442.1;0
}}
}}

Revision as of 19:32, 22 January 2013


Full id: C890_CD19_CD4_Peripheral_CD8_Natural_Dendritic_Mast



Phase1 CAGE Peaks

Hg19::chr12:12510270..12510289,+p5@LOH12CR1
Hg19::chr12:133065939..133065959,+p6@FBRSL1
Hg19::chr17:76356237..76356282,-p2@SOCS3
Hg19::chr19:54041603..54041615,+p10@ZNF331
Hg19::chr19:54041645..54041661,+p5@ZNF331
Hg19::chr20:34203794..34203818,+p8@SPAG4
Hg19::chrX:110924471..110924482,+p5@ALG13
Hg19::chrX:110924562..110924571,+p8@ALG13
Hg19::chrX:110924578..110924589,+p9@ALG13


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:0004577N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity0.0150712351348169
GO:0046627negative regulation of insulin receptor signaling pathway0.0188357167392016
GO:0030259lipid glycosylation0.0188357167392016
GO:0046626regulation of insulin receptor signaling pathway0.0188357167392016



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>

Cell Type
Ontology termp-valuen
classical monocyte7.84e-4242
CD14-positive, CD16-negative classical monocyte7.84e-4242
leukocyte2.11e-38136
myeloid leukocyte1.34e-3572
defensive cell1.39e-3448
phagocyte1.39e-3448
granulocyte monocyte progenitor cell1.07e-3067
hematopoietic lineage restricted progenitor cell1.33e-29120
myeloid lineage restricted progenitor cell3.84e-2866
macrophage dendritic cell progenitor4.21e-2861
nongranular leukocyte4.53e-28115
hematopoietic stem cell2.02e-27168
angioblastic mesenchymal cell2.02e-27168
hematopoietic cell3.14e-27177
monopoietic cell2.98e-2659
monocyte2.98e-2659
monoblast2.98e-2659
promonocyte2.98e-2659
hematopoietic oligopotent progenitor cell1.87e-23161
hematopoietic multipotent progenitor cell1.87e-23161
myeloid cell1.78e-20108
common myeloid progenitor1.78e-20108
stuff accumulating cell2.24e-1387
intermediate monocyte1.68e-099
CD14-positive, CD16-positive monocyte1.68e-099
CD4-positive, alpha-beta T cell5.15e-096
granulocyte1.70e-078
circulating cell5.05e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.31e-2898
blood island3.31e-2898
bone marrow3.94e-2776
bone element4.10e-2582
hemolymphoid system8.57e-25108
immune system2.65e-2493
skeletal element2.46e-2190
skeletal system1.61e-17100
adult organism1.14e-08114
lateral plate mesoderm3.14e-08203


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)
MA0003.12.34025
MA0004.10.415381
MA0006.15.76038
MA0007.10.397529
MA0009.10.870971
MA0014.10.841704
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
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.11.03929
MA0043.12.02319
MA0046.10.860127
MA0048.13.21312
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.22215
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.10.865474
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.0176541
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.714036
MA0105.10.854766
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.11.13131
MA0117.12.09924
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
MA0139.15.77823
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.10.39929
MA0146.12.57433
MA0147.12.52411
MA0148.10.439278
MA0149.10.464973
MA0062.20.421263
MA0035.20.473658
MA0039.21.17223
MA0138.20.608783
MA0002.20.152495
MA0137.20.780538
MA0104.22.15714
MA0047.20.542971
MA0112.20.674448
MA0065.20.408099
MA0150.15.50349
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.842081
MA0155.11.00468
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.60858
MA0160.10.453945
MA0161.10
MA0162.10.767014
MA0163.11.18882
MA0164.10.583138
MA0080.20.268439
MA0018.21.36887
MA0099.20.481058
MA0079.20.893499
MA0102.21.41188
MA0258.10.532421
MA0259.10.624802
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#1066463.573504248716680.002103883629372150.0121651811741777
CTCFL#14069048.776210826210820.0006740680382610040.00543915567086001
E2F6#187673.902232235764630.0003067423599492730.00316185011160108
EGR1#195884.433936973164571.92853122912633e-050.000435395315691148
ELK4#200547.215858514874680.001409539058987380.0091651631043197
GABPB1#255353.926491020101210.004337976092287310.0205840020491774
GTF2F1#296257.077589375976470.0002865435853580450.00304686677980135
HEY1#2346273.142308589082220.001258763462843770.0084575397128114
JUND#372764.663109294580680.0004849682005391460.00433755193081338
MYC#460963.48152124773960.002423669811459260.0136551573306896
PAX5#507964.446377020785220.0006322700088175870.00519091639422215
POLR2A#543081.908847268051620.0116612289598830.0425789984037065
POU2F2#545244.047166247885570.01161426156153230.0424342089636127
RAD21#588544.602237286869480.007351242900196250.0303953623363394
SETDB1#9869313.44000872600350.001144723251466790.00783702075778038
SMARCB1#659836.084238593719140.01075671401246010.0396968358567958
TAF1#687282.971596698440260.0004233749951234810.00395853725297236
TFAP2C#702244.804101604382320.006299303434747120.0277861617359274
USF1#739164.240999518138640.0008220017441944160.00625949982952392
ZEB1#693535.629477339181290.01330488236341950.0470347835071986
ZNF143#770257.500486973459950.0002177465175801830.00249137034942558



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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