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Coexpression cluster:C4751: Difference between revisions

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{{Coexpression_clusters
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0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,2.1595,0.494933,0.491742,0.63186,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,1.40888,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,1.7611,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,3.61775,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,1.44641,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,2.14035,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,6.48329,1.45054,3.91579,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.977977,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.946807,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,1.67826,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,3.46474,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,2.29164,0.318511,11.2136,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,2.84192,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;7.68548,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.24048,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,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;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;5.8296,MA0056.1;0,MA0057.1;1.59304,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;1.15625,MA0063.1;0,MA0066.1;2.1667,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;0.0185922,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;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.757898,MA0138.2;2.38017,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;1.2307,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;0.312019,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;2.76014,MA0163.1;3.96434,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.54885,MA0102.2;1.88331,MA0258.1;5.65409,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4751_Mast_Eosinophils_Neutrophils_granulocyte_Dendritic_mucinous_Smooth
|id=C4751
}}

Latest revision as of 14:19, 17 September 2013


Full id: C4751_Mast_Eosinophils_Neutrophils_granulocyte_Dendritic_mucinous_Smooth



Phase1 CAGE Peaks

Hg19::chr8:38644715..38644732,+p2@TACC1
Hg19::chr8:38644746..38644761,+p1@TACC1
Hg19::chr8:38644778..38644785,+p14@TACC1


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
leukocyte1.01e-37136
myeloid leukocyte1.76e-3472
granulocyte monocyte progenitor cell4.12e-3167
hematopoietic lineage restricted progenitor cell4.99e-30120
myeloid lineage restricted progenitor cell1.22e-2966
macrophage dendritic cell progenitor2.44e-2761
monopoietic cell3.85e-2659
monocyte3.85e-2659
monoblast3.85e-2659
promonocyte3.85e-2659
hematopoietic stem cell4.05e-26168
angioblastic mesenchymal cell4.05e-26168
nongranular leukocyte4.26e-26115
defensive cell9.61e-2548
phagocyte9.61e-2548
hematopoietic cell2.15e-24177
hematopoietic oligopotent progenitor cell2.97e-24161
hematopoietic multipotent progenitor cell2.97e-24161
classical monocyte1.15e-2342
CD14-positive, CD16-negative classical monocyte1.15e-2342
myeloid cell1.69e-21108
common myeloid progenitor1.69e-21108
multi fate stem cell1.15e-11427
mesenchymal cell8.86e-11354
somatic stem cell3.69e-10433
connective tissue cell3.97e-10361
motile cell5.27e-10386
stem cell1.43e-09441
stuff accumulating cell2.25e-0887
Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.59e-32108
immune system1.48e-3193
hematopoietic system1.22e-3098
blood island1.22e-3098
bone marrow5.42e-2976
bone element3.28e-2682
skeletal system3.09e-21100
skeletal element4.78e-2190
lateral plate mesoderm5.00e-20203
musculoskeletal system1.78e-16167
mesoderm2.18e-14315
mesoderm-derived structure2.18e-14315
presumptive mesoderm2.18e-14315
connective tissue7.55e-11371


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)
MA0003.17.68548
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.15.8296
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.22.38017
MA0002.21.20011
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.23.77966
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
MA0102.21.88331
MA0258.15.65409
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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139564680217675
CCNT2#90536.336201576962630.003930750035764890.0191297112295084
CTCF#1066435.360256373075030.0064925092527670.028149749827704
E2F1#186934.907389214879320.008460985347239390.0327936186699449
E2F4#1874312.66806031528440.0004917987006298980.00439187383455203
EGR1#195834.988179094810140.008056488137383440.0322676623937793
ELF1#199734.258097958807540.01295179875054610.0465171742394265
EP300#203336.77394172622320.003216880500103790.0168565442050243
FOXA1#3169311.08141974938550.000734755275698670.00584441022381518
GATA1#2623313.56030814380040.0004009615963782630.00389616934910211
HMGN3#932438.178547723350590.001827766942164210.010929242624109
IRF1#365937.63716375356390.002244692747297240.0128795443267211
JUND#372736.994663941871030.002921845042734990.0157743383002429
MAX#414936.452555509007120.003721913834265510.0187485148766148
NANOG#79923329.24477848101273.99627955670032e-050.000741722837430647
NFKB1#479035.488063424193840.006049381815655430.0270934168465731
NRF1#4899312.21027944771090.0005492172401020010.00473773018410943
PAX5#507936.669565531177830.003370290999677260.0173736338457697
POU2F2#545239.106124057742520.001324165192682130.00885935224590192
REST#597839.650028716128020.001112636247114590.00771648960836713
SIN3A#2594235.408884726815140.006318961977991520.0278423013972686
SIX5#147912317.0867153554590.0002004060546325010.00240356085665638
SP1#666735.69838137814090.005403962701712170.0248026570250106
SPI1#668838.204323508522730.001810593189410520.0109449870989666
SRF#6722313.79717826216780.0003806615025800190.00376619047631249
TAF7#6879311.43306940492390.0006690181981945830.00545999778082707
TAL1#6886329.86861667744023.75103522793067e-050.000723060849335273
TCF7L2#6934310.77017656313730.0008003181298398380.00617771065501425
USF1#739136.361499277207960.00388404057290560.0191278970808548
YY1#752834.911170749853860.008441455341808260.0331397644793111
ZBTB7A#5134137.35190930787590.002516255860282270.0141029969835795



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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