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Coexpression cluster:C2036: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,1.42265,0.741427,0.534346,0.739643,3.1911,0.395818,1.01802,0.462021,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,1.18793,0.938585,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.911389,0.49475,0.285913,0.491074,0.740899,2.0411,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,1.34056,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,1.03184,1.27559,0.109222,1.84544,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,1.17564,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.393155,0.681522,2.26288,1.1313,1.31973,0.932085,0.736652,3.29893,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,2.16698,0.676268,1.73115,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,0.437774,0.234974,0.175846,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,1.42265,0.741427,0.534346,0.739643,3.1911,0.395818,1.01802,0.462021,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,1.18793,0.938585,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.911389,0.49475,0.285913,0.491074,0.740899,2.0411,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,1.34056,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,1.03184,1.27559,0.109222,1.84544,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,1.17564,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.393155,0.681522,2.26288,1.1313,1.31973,0.932085,0.736652,3.29893,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,2.16698,0.676268,1.73115,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,0.437774,0.234974,0.175846,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.34758,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.709734,MA0050.1;2.80362,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;1.47051,MA0060.1;1.01899,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;3.20115,MA0069.1;2.67291,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;6.26196,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;4.40632,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.70272,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;3.05702,MA0039.2;3.07509,MA0138.2;0.928035,MA0002.2;1.75253,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;1.09513,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.02191,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;1.1691,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;4.43857,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:22, 22 January 2013


Full id: C2036_CD34_chronic_migratory_Melanocyte_Mast_acute_heart



Phase1 CAGE Peaks

Hg19::chr10:11207051..11207081,+p2@CELF2
Hg19::chr10:11207088..11207095,+p17@CELF2
Hg19::chr10:11207117..11207128,+p14@CELF2
Hg19::chr10:11207157..11207175,+p13@CELF2


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 cell8.55e-57168
angioblastic mesenchymal cell8.55e-57168
hematopoietic cell8.04e-53177
hematopoietic oligopotent progenitor cell2.50e-52161
hematopoietic multipotent progenitor cell2.50e-52161
leukocyte1.21e-40136
myeloid cell6.94e-34108
common myeloid progenitor6.94e-34108
hematopoietic lineage restricted progenitor cell1.37e-30120
nongranular leukocyte1.61e-29115
myeloid leukocyte9.68e-1872
T cell5.69e-1725
pro-T cell5.69e-1725
granulocyte monocyte progenitor cell2.60e-1667
lymphoid lineage restricted progenitor cell5.25e-1652
lymphocyte5.55e-1653
common lymphoid progenitor5.55e-1653
nucleate cell1.07e-1455
myeloid lineage restricted progenitor cell6.66e-1466
mature alpha-beta T cell1.69e-1318
alpha-beta T cell1.69e-1318
immature T cell1.69e-1318
mature T cell1.69e-1318
immature alpha-beta T cell1.69e-1318
macrophage dendritic cell progenitor9.27e-1361
defensive cell3.26e-1248
phagocyte3.26e-1248
monopoietic cell4.75e-1259
monocyte4.75e-1259
monoblast4.75e-1259
promonocyte4.75e-1259
classical monocyte2.32e-1142
CD14-positive, CD16-negative classical monocyte2.32e-1142
mesenchymal cell2.53e-10354
motile cell3.28e-09386
connective tissue cell3.41e-09361
CD8-positive, alpha-beta T cell1.63e-0811
stuff accumulating cell2.01e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.63e-2298
blood island3.63e-2298
hemolymphoid system8.46e-19108
adult organism6.33e-17114
bone marrow3.59e-1376
immune system8.13e-1393
bone element3.07e-1182
neural tube1.80e-0956
neural rod1.80e-0956
future spinal cord1.80e-0956
neural keel1.80e-0956
regional part of forebrain6.34e-0941
forebrain6.34e-0941
anterior neural tube6.34e-0941
future forebrain6.34e-0941
brain grey matter1.20e-0834
gray matter1.20e-0834
regional part of nervous system1.49e-0853
regional part of brain1.49e-0853
skeletal element1.58e-0890
telencephalon1.70e-0834
blood2.07e-0815
haemolymphatic fluid2.07e-0815
organism substance2.07e-0815
cerebral hemisphere2.48e-0832
regional part of telencephalon2.92e-0832
connective tissue5.46e-08371
Disease
Ontology termp-valuen
leukemia5.18e-1939
hematologic cancer1.69e-1651
immune system cancer1.69e-1651
myeloid leukemia3.97e-1631


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.12.80362
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.11.47051
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.13.20115
MA0069.12.67291
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.16.26196
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.14.40632
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.23.05702
MA0039.23.07509
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.24.43857
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
E2F6#187645.017155731697390.00157802193473060.0099467096892588
FOS#235348.99795530889440.0001525147711168630.00194510809386666
FOSL1#8061439.7135797163734.01511434669553e-071.93509241926412e-05
HEY1#2346244.040111043105710.00375304636917980.0185439944055812
MAX#414946.452555509007120.0005767613195645490.00484254163952102
NRF1#4899412.21027944771094.49717228915276e-050.00079150687008228
PAX5#507946.669565531177830.0005052774169483260.00442892724705549
POU2F2#545249.106124057742520.000145395665174930.00187956156395649
SIN3A#2594245.408884726815140.001168172384885160.00793823643080362
TAF1#687243.343046285745290.008005664898701650.0321035031621679
TAL1#6886429.86861667744021.25525650806991e-065.02868179694335e-05
TBP#690843.706770687096390.005296377814784350.0243366801266339
YY1#752844.911170749853860.00171871838055440.0106585849383481
ZNF263#1012748.221841637010680.0002187871180958320.00247964273758118



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:C2036&oldid=2570547"