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Coexpression cluster:C4332: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,2.14419,0.491742,4.31458,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,1.11965,1.46099,5.03488,0.596053,0.855276,1.39264,4.13908,0.598234,0.777097,0.718382,0.63803,0.901413,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,1.10051,1.06461,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,2.84649,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,2.82056,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,8.95585
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,2.14419,0.491742,4.31458,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,1.11965,1.46099,5.03488,0.596053,0.855276,1.39264,4.13908,0.598234,0.777097,0.718382,0.63803,0.901413,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,1.10051,1.06461,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,2.84649,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,2.82056,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,8.95585
|tfbs_overrepresentation_jaspar=MA0003.1;2.61626,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;2.44638,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;2.45333,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0834661,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;1.16674,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.62945,MA0138.2;1.04628,MA0002.2;2.08438,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;3.77966,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;4.10519,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:59, 22 January 2013


Full id: C4332_CD14CD16_Alveolar_Eosinophils_CD14_immature_Natural_CD4



Phase1 CAGE Peaks

Hg19::chr3:47021200..47021229,+p3@NBEAL2
Hg19::chr3:47021263..47021333,+p1@NBEAL2
Hg19::chr3:47021336..47021347,+p9@NBEAL2


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 cell1.55e-48168
angioblastic mesenchymal cell1.55e-48168
hematopoietic oligopotent progenitor cell3.22e-47161
hematopoietic multipotent progenitor cell3.22e-47161
hematopoietic cell2.94e-46177
leukocyte1.63e-43136
nongranular leukocyte2.60e-35115
hematopoietic lineage restricted progenitor cell3.30e-34120
myeloid cell3.25e-31108
common myeloid progenitor3.25e-31108
myeloid leukocyte1.13e-2472
defensive cell1.31e-2248
phagocyte1.31e-2248
granulocyte monocyte progenitor cell6.22e-2267
classical monocyte9.59e-2242
CD14-positive, CD16-negative classical monocyte9.59e-2242
macrophage dendritic cell progenitor1.31e-2061
monopoietic cell1.26e-1959
monocyte1.26e-1959
monoblast1.26e-1959
promonocyte1.26e-1959
myeloid lineage restricted progenitor cell4.64e-1966
lymphocyte5.12e-1453
common lymphoid progenitor5.12e-1453
lymphoid lineage restricted progenitor cell8.24e-1452
nucleate cell6.19e-1355
T cell2.64e-1025
pro-T cell2.64e-1025
mature alpha-beta T cell1.51e-0918
alpha-beta T cell1.51e-0918
immature T cell1.51e-0918
mature T cell1.51e-0918
immature alpha-beta T cell1.51e-0918
stuff accumulating cell1.35e-0787
endothelial cell1.80e-0736
intermediate monocyte2.18e-079
CD14-positive, CD16-positive monocyte2.18e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.25e-2398
blood island5.25e-2398
hemolymphoid system3.33e-22108
immune system7.22e-1793
bone marrow6.96e-1676
bone element6.34e-1482
skeletal element1.70e-1090
lateral plate mesoderm1.15e-09203
skeletal system2.72e-07100
blood9.16e-0715
haemolymphatic fluid9.16e-0715
organism substance9.16e-0715
Disease
Ontology termp-valuen
leukemia8.67e-0739
hematologic cancer8.73e-0751
immune system cancer8.73e-0751


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.22.08438
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.23.77966
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.10519
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CCNT2#90536.336201576962630.003930750035764890.0190675152338713
CTCF#1066435.360256373075030.0064925092527670.0280565695899426
E2F4#1874312.66806031528440.0004917987006298980.00438175776276113
EBF1#187938.9064668465690.00141523283560980.00917761577884212
ELF1#199734.258097958807540.01295179875054610.0463943239713364
ETS1#211339.728760922202340.001085840092584840.00763972335148664
GTF2B#2959331.94382993432423.06634405746243e-050.000628919691707225
HMGN3#932438.178547723350590.001827766942164210.0108968005293235
IRF1#365937.63716375356390.002244692747297240.012847781324874
JUND#372736.994663941871030.002921845042734990.0157263746865698
MYC#460935.22228187160940.007020843755740150.0295462747715576
SMC3#9126315.04493284493280.0002935825420371870.00310150385472605
SP1#666735.69838137814090.005403962701712170.0247363455734624
SPI1#668838.204323508522730.001810593189410520.0109279092758232
TCF12#6938310.63446490218640.0008313523990202070.00630633448585643
THAP1#55145220.91276306856750.002983447413736940.0158738735770173
YY1#752834.911170749853860.008441455341808260.0330478372546805
ZBTB7A#5134137.35190930787590.002516255860282270.0140629981159105
ZNF143#7702313.50087655222790.0004062804962997170.0039003151717112
ZNF263#1012738.221841637010680.001799043925565870.0109755446312386



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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