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Coexpression cluster:C2609: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,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;1.92746,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.69331,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;1.68681,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;1.52107,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;2.83685,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;1.62583,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;1.33363,MA0103.1;0.521546,MA0105.1;0.656404,MA0106.1;9.62372,MA0107.1;1.1497,MA0108.2;1.03412,MA0109.1;0,MA0111.1;2.66544,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;1.63368,MA0140.1;0.779643,MA0141.1;1.46638,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.569905,MA0146.1;0.481,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;1.83323,MA0039.2;2.52211,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;1.21162,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;3.02177,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;2.72671,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:47, 22 January 2013


Full id: C2609_Dendritic_anaplastic_Neutrophils_hairy_migratory_adult_acute



Phase1 CAGE Peaks

Hg19::chr20:23029233..23029266,-p2@THBD
Hg19::chr9:139926533..139926546,-p1@FUT7
Hg19::chr9:139926550..139926561,-p2@FUT7
Hg19::chr9:139926567..139926578,-p4@FUT7


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:0032496response to lipopolysaccharide0.00793183603597481
GO:0046920alpha(1,3)-fucosyltransferase activity0.00793183603597481
GO:0010165response to X-ray0.00793183603597481
GO:0019317fucose catabolic process0.00793183603597481
GO:0042355L-fucose catabolic process0.00793183603597481
GO:0002237response to molecule of bacterial origin0.00793183603597481
GO:0042354L-fucose metabolic process0.00793183603597481
GO:0051591response to cAMP0.00793183603597481
GO:0010212response to ionizing radiation0.00833218849866979
GO:0006004fucose metabolic process0.00865240253491506
GO:0008417fucosyltransferase activity0.00943856771636449
GO:0010033response to organic substance0.0297820990700115
GO:0007565female pregnancy0.033923185148474
GO:0007596blood coagulation0.033923185148474
GO:0009314response to radiation0.033923185148474
GO:0050817coagulation0.033923185148474
GO:0007599hemostasis0.033923185148474
GO:0009617response to bacterium0.033923185148474
GO:0050878regulation of body fluid levels0.0377176375041188
GO:0042060wound healing0.0377176375041188
GO:0019320hexose catabolic process0.0380163926467462
GO:0046365monosaccharide catabolic process0.0380163926467462
GO:0046164alcohol catabolic process0.0380163926467462
GO:0009628response to abiotic stimulus0.0380163926467462
GO:0006486protein amino acid glycosylation0.0380163926467462
GO:0043413biopolymer glycosylation0.0380163926467462
GO:0009101glycoprotein biosynthetic process0.0380163926467462
GO:0044275cellular carbohydrate catabolic process0.0380163926467462
GO:0016052carbohydrate catabolic process0.0380904031704503
GO:0051707response to other organism0.0385932546624681
GO:0009100glycoprotein metabolic process0.0385932546624681
GO:0009790embryonic development0.0422235260882838
GO:0019318hexose metabolic process0.0461195912984867
GO:0005996monosaccharide metabolic process0.0461195912984867
GO:0016758transferase activity, transferring hexosyl groups0.0461195912984867
GO:0009607response to biotic stimulus0.0461195912984867
GO:0022414reproductive process0.047346240696365



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 cell5.59e-60168
angioblastic mesenchymal cell5.59e-60168
hematopoietic cell3.16e-55177
hematopoietic oligopotent progenitor cell5.45e-54161
hematopoietic multipotent progenitor cell5.45e-54161
leukocyte4.31e-52136
nongranular leukocyte2.44e-35115
hematopoietic lineage restricted progenitor cell5.77e-34120
myeloid cell8.85e-29108
common myeloid progenitor8.85e-29108
lymphocyte4.77e-2353
common lymphoid progenitor4.77e-2353
lymphoid lineage restricted progenitor cell2.59e-2252
nucleate cell9.28e-2255
myeloid leukocyte1.57e-1872
T cell1.13e-1625
pro-T cell1.13e-1625
dendritic cell1.80e-1510
mature alpha-beta T cell4.52e-1518
alpha-beta T cell4.52e-1518
immature T cell4.52e-1518
mature T cell4.52e-1518
immature alpha-beta T cell4.52e-1518
granulocyte monocyte progenitor cell3.17e-1467
mesenchymal cell4.32e-13354
conventional dendritic cell1.19e-128
macrophage dendritic cell progenitor1.59e-1261
connective tissue cell2.67e-12361
granulocyte1.76e-118
myeloid lineage restricted progenitor cell2.66e-1166
monopoietic cell4.77e-1159
monocyte4.77e-1159
monoblast4.77e-1159
promonocyte4.77e-1159
motile cell1.40e-09386
immature conventional dendritic cell7.44e-095
common dendritic progenitor7.44e-095
CD8-positive, alpha-beta T cell4.29e-0811
classical monocyte5.46e-0842
CD14-positive, CD16-negative classical monocyte5.46e-0842
defensive cell7.70e-0848
phagocyte7.70e-0848
blood cell9.16e-0811
Langerhans cell9.86e-085
CD4-positive, alpha-beta T cell1.23e-076
lymphocyte of B lineage4.92e-0724
pro-B cell4.92e-0724
multi fate stem cell8.71e-07427
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.69e-2698
blood island5.69e-2698
hemolymphoid system2.59e-24108
immune system1.54e-1593
bone marrow4.43e-1376
blood2.54e-1215
haemolymphatic fluid2.54e-1215
organism substance2.54e-1215
connective tissue1.17e-11371
bone element2.46e-1182
skeletal element2.06e-0990
skeletal system1.67e-07100
Disease
Ontology termp-valuen
leukemia5.25e-1039
hematologic cancer8.17e-1051
immune system cancer8.17e-1051
myeloid leukemia1.69e-0831


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
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
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.12.83685
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.656404
MA0106.19.62372
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.12.66544
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
MA0139.11.63368
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.21.83323
MA0039.22.52211
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.13.02177
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.72671
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
GABPB1#255335.300762877136630.01012678824234270.037868582378246
HDAC2#3066310.06171517746970.00156372754474740.00992549781487016
SPI1#668836.153242631392040.006580387113059030.0281037478408756
TCF12#693837.975848676639820.003090920396013070.0162814664467246



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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