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Coexpression cluster:C4132: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,1.7611,1.00973,0.409304,0.842925,1.55576,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,3.5962,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,3.40847,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.06461,0.396746,1.12884,2.69227,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.22068,0.303648,0.381882,1.053,2.0169,1.63834,3.03421,1.23218,1.34254,0.642354,0.560075,0.450952,2.84649,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,1.7611,1.00973,0.409304,0.842925,1.55576,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,3.5962,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,3.40847,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.06461,0.396746,1.12884,2.69227,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.22068,0.303648,0.381882,1.053,2.0169,1.63834,3.03421,1.23218,1.34254,0.642354,0.560075,0.450952,2.84649,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224
|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;3.90467,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;0.341392,MA0050.1;3.16043,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,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;1.84332,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;13.9778,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;2.37746,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,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;1.80901,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;2.36034,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;1.37817,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;2.15877,MA0138.2;3.88672,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;1.34467,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;1.51687,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;2.08754,MA0079.2;4.10519,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:51, 22 January 2013


Full id: C4132_cord_Mast_mature_CD14_Neutrophils_Eosinophils_CD8



Phase1 CAGE Peaks

Hg19::chr2:145274900..145274934,-p4@ZEB2
Hg19::chr2:145274981..145274994,-p9@ZEB2
Hg19::chr2:145274998..145275012,-p13@ZEB2


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>

Cell Type
Ontology termp-valuen
myeloid leukocyte3.16e-3172
myeloid lineage restricted progenitor cell2.19e-2766
classical monocyte3.09e-2542
CD14-positive, CD16-negative classical monocyte3.09e-2542
myeloid cell5.66e-25108
common myeloid progenitor5.66e-25108
defensive cell1.19e-2448
phagocyte1.19e-2448
granulocyte monocyte progenitor cell1.24e-2467
monopoietic cell1.47e-2359
monocyte1.47e-2359
monoblast1.47e-2359
promonocyte1.47e-2359
macrophage dendritic cell progenitor8.75e-2361
leukocyte6.58e-22136
hematopoietic stem cell1.00e-19168
angioblastic mesenchymal cell1.00e-19168
hematopoietic cell2.26e-19177
hematopoietic oligopotent progenitor cell7.29e-19161
hematopoietic multipotent progenitor cell7.29e-19161
mesenchymal cell4.48e-17354
hematopoietic lineage restricted progenitor cell5.66e-17120
motile cell3.87e-16386
connective tissue cell7.61e-16361
nongranular leukocyte1.35e-15115
multi fate stem cell2.34e-15427
stuff accumulating cell2.72e-1587
somatic stem cell2.92e-14433
stem cell3.28e-13441
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.53e-2798
blood island1.53e-2798
bone marrow4.76e-2376
bone element3.08e-2282
hemolymphoid system4.06e-22108
skeletal system3.29e-19100
skeletal element4.53e-1890
adult organism2.65e-17114
connective tissue1.33e-16371
immune system3.30e-1693
regional part of forebrain2.24e-1441
forebrain2.24e-1441
anterior neural tube2.24e-1441
future forebrain2.24e-1441
tissue2.24e-14773
telencephalon3.09e-1434
musculoskeletal system3.28e-14167
neural tube4.98e-1456
neural rod4.98e-1456
future spinal cord4.98e-1456
neural keel4.98e-1456
brain grey matter6.90e-1434
gray matter6.90e-1434
central nervous system9.30e-1481
nervous system2.70e-1389
regional part of nervous system3.52e-1353
regional part of brain3.52e-1353
cerebral hemisphere3.84e-1332
regional part of telencephalon4.65e-1332
brain1.67e-1268
future brain1.67e-1268
lateral plate mesoderm3.96e-10203
cerebral cortex5.10e-1025
pallium5.10e-1025
regional part of cerebral cortex5.32e-1022
neural plate1.12e-0982
presumptive neural plate1.12e-0982
neocortex3.42e-0920
neurectoderm5.77e-0986
pre-chordal neural plate2.57e-0861
blood1.25e-0715
haemolymphatic fluid1.25e-0715
organism substance1.25e-0715
structure with developmental contribution from neural crest5.23e-07132
mesoderm9.59e-07315
mesoderm-derived structure9.59e-07315
presumptive mesoderm9.59e-07315


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)
MA0003.11.0927
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
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
MA0048.10.341392
MA0050.13.16043
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
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
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.113.9778
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.12.37746
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
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
MA0145.11.37817
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.23.88672
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.22.08754
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
BATF#10538324.35780179230366.91705216281876e-050.00110039605610454
CEBPB#105137.971147625824820.001974187055288560.0115443517282912
FOS#235338.99795530889440.001372499272417130.00899149739756445
FOSL1#8061339.7135797163731.59554825631833e-050.000371626816105331
GATA1#2623313.56030814380040.0004009615963782630.00388460372580236
GATA2#2624312.7449317335540.0004829527704283790.00437497652795295
JUN#3725312.51282919233630.0005103313992726250.00444932807485046
JUNB#3726330.61063265982113.4847716247536e-050.000681164259250686
JUND#372736.994663941871030.002921845042734990.0157053306442717
NR3C1#2908314.9730233311730.0002978331194675480.00309321729952976
RAD21#5885310.35503389545630.0009004912073565420.00665391263655793
STAT3#6774310.51946499715420.0008589184530415310.0064359724721771
TFAP2A#7020316.5186343730450.0002218033880766340.00248684101420672
TFAP2C#7022310.80922860986020.0007916746575753130.00616889573696248
YY1#752834.911170749853860.008441455341808260.033002064626904



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4132&oldid=2572643"