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Coexpression cluster:C2568: Difference between revisions

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{{Coexpression_clusters
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large ribosomal subunit (sensu Eukaryota)!5.52188315379147e-05!6164;6130$GO:0005830!cytosolic ribosome (sensu Eukaryota)!0.000103395585369577!6164;6130$GO:0015934!large ribosomal subunit!0.000135625200268563!6164;6130$GO:0044445!cytosolic part!0.000334498691046984!6164;6130$GO:0033279!ribosomal subunit!0.000372239011198639!6164;6130$GO:0042788!polysomal ribosome!0.00168758983169338!6130$GO:0005829!cytosol!0.00171424291592199!6164;6130$GO:0003735!structural constituent of ribosome!0.00253119844918806!6164;6130$GO:0005844!polysome!0.00253119844918806!6130$GO:0005840!ribosome!0.00268251742263055!6164;6130$GO:0003723!RNA binding!0.00322991211205015!6164;6130$GO:0030529!ribonucleoprotein complex!0.00401754259108733!6164;6130$GO:0006412!translation!0.0041720570111862!6164;6130$GO:0009059!macromolecule biosynthetic process!0.00650588975790638!6164;6130$GO:0044249!cellular biosynthetic process!0.00932462001903585!6164;6130$GO:0009058!biosynthetic process!0.0140181638787613!6164;6130$GO:0042254!ribosome biogenesis and assembly!0.0165024219924451!6130$GO:0043232!intracellular non-membrane-bound organelle!0.016714845025811!6164;6130$GO:0043228!non-membrane-bound organelle!0.016714845025811!6164;6130$GO:0032991!macromolecular complex!0.0276252430289505!6164;6130$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0276252430289505!6130$GO:0044446!intracellular organelle part!0.0276252430289505!6164;6130$GO:0044422!organelle part!0.0276252430289505!6164;6130$GO:0044444!cytoplasmic part!0.0327293167586561!6164;6130$GO:0010467!gene expression!0.0441384679540688!6164;6130$GO:0044267!cellular protein metabolic process!0.0441384679540688!6164;6130$GO:0044260!cellular macromolecule metabolic process!0.0441384679540688!6164;6130$GO:0019538!protein metabolic process!0.0456568104643413!6164;6130|id=C2568|ontology_enrichment_celltype=CL:0000003!3.31e-26!722;CL:0000988!6.53e-21!177;CL:0002371!1.37e-20!588;CL:0000037!2.39e-20!168;CL:0000566!2.39e-20!168;CL:0002031!3.02e-20!120;CL:0000034!6.97e-20!441;CL:0002087!3.50e-19!115;CL:0002032!4.21e-19!161;CL:0000837!4.21e-19!161;CL:0000048!5.85e-19!427;CL:0000723!2.16e-18!433;CL:0002320!3.24e-18!361;CL:0000548!5.72e-18!679;CL:0000255!5.72e-18!679;CL:0000860!1.04e-17!42;CL:0002057!1.04e-17!42;CL:0000738!1.06e-17!136;CL:0000134!8.15e-17!354;CL:0000219!8.94e-15!386;CL:0000473!2.82e-14!48;CL:0000234!2.82e-14!48;CL:0002242!8.08e-11!55;CL:0000838!1.02e-10!52;CL:0000542!2.10e-10!53;CL:0000051!2.10e-10!53;CL:0002009!6.61e-10!61;CL:0000325!1.48e-09!87;CL:0000763!1.69e-09!108;CL:0000049!1.69e-09!108;CL:0000839!2.33e-09!66;CL:0000557!3.90e-09!67;CL:0002194!3.90e-09!59;CL:0000576!3.90e-09!59;CL:0000040!3.90e-09!59;CL:0000559!3.90e-09!59;CL:0000791!1.04e-07!18;CL:0000789!1.04e-07!18;CL:0002420!1.04e-07!18;CL:0002419!1.04e-07!18;CL:0000790!1.04e-07!18;CL:0000236!1.69e-07!14;CL:0000084!6.53e-07!25;CL:0000827!6.53e-07!25;CL:0000766!8.84e-07!72|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002384!1.17e-17!371;UBERON:0004765!1.49e-10!90;UBERON:0002371!2.33e-10!76;UBERON:0002390!1.51e-09!98;UBERON:0003061!1.51e-09!98;UBERON:0002193!1.58e-09!108;UBERON:0001474!1.83e-09!82;UBERON:0001434!2.39e-08!100;UBERON:0002405!2.70e-08!93;UBERON:0002204!5.54e-07!167;UBERON:0003081!8.10e-07!203|pathway_enrichment=1.02743394677841e-05;0.00315487951907255;2;92;Ribosome (KEGG):03010!1.05001491264167e-05;0.00315487951907255;2;93;Cytoplasmic Ribosomal Proteins (Wikipathways):WP477!0.000107161409738044;0.0107682553184368;2;296;Metabolism of proteins (Reactome):REACT_17015!1.58091305570944e-05;0.00315487951907255;2;114;Regulation of beta-cell development (Reactome):REACT_13698!0.000216998173040322;0.0171699804418155;2;421;Gene Expression (Reactome):REACT_71!0.000119080232589348;0.0107682553184368;2;312;Diabetes pathways (Reactome):REACT_15380!2.49200593923582e-05;0.00315487951907255;2;143;Influenza Infection (Reactome):REACT_6167!2.32019424245013e-05;0.00315487951907255;2;138;{RPS27A,138} (Static 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.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.505745,1.73475,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,1.10579,0.344471,0.49475,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.99221,1.33034,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,1.17564,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,3.02112,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.359498|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,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;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.214613,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;1.13665,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;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.8309,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.931615,MA0035.2;0.778873,MA0039.2;0.257871,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0270533,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2568_CD4_Smooth_Aortic_acute_CD34_Fibroblast_CD8
|id=C2568
}}

Latest revision as of 12:08, 17 September 2013


Full id: C2568_CD4_Smooth_Aortic_acute_CD34_Fibroblast_CD8



Phase1 CAGE Peaks

Hg19::chr1:22234543..22234549,+p1@ENST00000423231
Hg19::chr1:53238346..53238348,-p1@ENST00000437890
Hg19::chr4:109541723..109541738,+p1@RPL34
Hg19::chr9:136215044..136215086,+p1@RPL7A


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

p.valueFDRnGenesnPathwayName
1.02743394677841e-050.00315487951907255292Ribosome (KEGG):03010
1.05001491264167e-050.00315487951907255293Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
0.0001071614097380440.01076825531843682296Metabolism of proteins (Reactome):REACT_17015
1.58091305570944e-050.003154879519072552114Regulation of beta-cell development (Reactome):REACT_13698
0.0002169981730403220.01716998044181552421Gene Expression (Reactome):REACT_71
0.0001190802325893480.01076825531843682312Diabetes pathways (Reactome):REACT_15380
2.49200593923582e-050.003154879519072552143Influenza Infection (Reactome):REACT_6167
2.32019424245013e-050.003154879519072552138{RPS27A,138} (Static Module):NA



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:0005842cytosolic large ribosomal subunit (sensu Eukaryota)5.52188315379147e-05
GO:0005830cytosolic ribosome (sensu Eukaryota)0.000103395585369577
GO:0015934large ribosomal subunit0.000135625200268563
GO:0044445cytosolic part0.000334498691046984
GO:0033279ribosomal subunit0.000372239011198639
GO:0042788polysomal ribosome0.00168758983169338
GO:0005829cytosol0.00171424291592199
GO:0003735structural constituent of ribosome0.00253119844918806
GO:0005844polysome0.00253119844918806
GO:0005840ribosome0.00268251742263055
GO:0003723RNA binding0.00322991211205015
GO:0030529ribonucleoprotein complex0.00401754259108733
GO:0006412translation0.0041720570111862
GO:0009059macromolecule biosynthetic process0.00650588975790638
GO:0044249cellular biosynthetic process0.00932462001903585
GO:0009058biosynthetic process0.0140181638787613
GO:0042254ribosome biogenesis and assembly0.0165024219924451
GO:0043232intracellular non-membrane-bound organelle0.016714845025811
GO:0043228non-membrane-bound organelle0.016714845025811
GO:0032991macromolecular complex0.0276252430289505
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0276252430289505
GO:0044446intracellular organelle part0.0276252430289505
GO:0044422organelle part0.0276252430289505
GO:0044444cytoplasmic part0.0327293167586561
GO:0010467gene expression0.0441384679540688
GO:0044267cellular protein metabolic process0.0441384679540688
GO:0044260cellular macromolecule metabolic process0.0441384679540688
GO:0019538protein metabolic process0.0456568104643413



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
native cell3.31e-26722
hematopoietic cell6.53e-21177
somatic cell1.37e-20588
hematopoietic stem cell2.39e-20168
angioblastic mesenchymal cell2.39e-20168
hematopoietic lineage restricted progenitor cell3.02e-20120
stem cell6.97e-20441
nongranular leukocyte3.50e-19115
hematopoietic oligopotent progenitor cell4.21e-19161
hematopoietic multipotent progenitor cell4.21e-19161
multi fate stem cell5.85e-19427
somatic stem cell2.16e-18433
connective tissue cell3.24e-18361
animal cell5.72e-18679
eukaryotic cell5.72e-18679
classical monocyte1.04e-1742
CD14-positive, CD16-negative classical monocyte1.04e-1742
leukocyte1.06e-17136
mesenchymal cell8.15e-17354
motile cell8.94e-15386
defensive cell2.82e-1448
phagocyte2.82e-1448
nucleate cell8.08e-1155
lymphoid lineage restricted progenitor cell1.02e-1052
lymphocyte2.10e-1053
common lymphoid progenitor2.10e-1053
macrophage dendritic cell progenitor6.61e-1061
stuff accumulating cell1.48e-0987
myeloid cell1.69e-09108
common myeloid progenitor1.69e-09108
myeloid lineage restricted progenitor cell2.33e-0966
granulocyte monocyte progenitor cell3.90e-0967
monopoietic cell3.90e-0959
monocyte3.90e-0959
monoblast3.90e-0959
promonocyte3.90e-0959
mature alpha-beta T cell1.04e-0718
alpha-beta T cell1.04e-0718
immature T cell1.04e-0718
mature T cell1.04e-0718
immature alpha-beta T cell1.04e-0718
B cell1.69e-0714
T cell6.53e-0725
pro-T cell6.53e-0725
myeloid leukocyte8.84e-0772
Uber Anatomy
Ontology termp-valuen
connective tissue1.17e-17371
skeletal element1.49e-1090
bone marrow2.33e-1076
hematopoietic system1.51e-0998
blood island1.51e-0998
hemolymphoid system1.58e-09108
bone element1.83e-0982
skeletal system2.39e-08100
immune system2.70e-0893
musculoskeletal system5.54e-07167
lateral plate mesoderm8.10e-07203


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
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
MA0114.11.13665
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
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0270533
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
BRCA1#672210.09211532161190.0137713969900260.0484739621260263
KAT2A#26481154.02250.006476819949311040.0281249261438649
ZZZ3#260092119.7066062176170.0001039630683859570.00145254834771385



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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