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Coexpression cluster:C3615: Difference between revisions

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{{Coexpression_clusters
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part!0.00640195440246109!23293;1060$GO:0005694!chromosome!0.00640195440246109!23293;1060$GO:0005697!telomerase holoenzyme complex!0.00640195440246109!23293$GO:0035303!regulation of dephosphorylation!0.00640195440246109!23293$GO:0042162!telomeric DNA binding!0.0122082852453962!23293$GO:0000184!mRNA catabolic process, nonsense-mediated decay!0.0122082852453962!23293$GO:0006406!mRNA export from nucleus!0.0122082852453962!23293$GO:0032200!telomere organization and biogenesis!0.0122082852453962!23293$GO:0006402!mRNA catabolic process!0.0122082852453962!23293$GO:0000723!telomere maintenance!0.0122082852453962!23293$GO:0006405!RNA export from nucleus!0.0122082852453962!23293$GO:0000781!chromosome, telomeric region!0.0122082852453962!23293$GO:0000776!kinetochore!0.0122082852453962!1060$GO:0051168!nuclear export!0.0156966496204888!23293$GO:0006401!RNA catabolic process!0.0156966496204888!23293$GO:0051174!regulation of phosphorus metabolic process!0.0204600198138956!23293$GO:0019220!regulation of phosphate metabolic process!0.0204600198138956!23293$GO:0000775!chromosome, pericentric region!0.0204600198138956!1060$GO:0051028!mRNA transport!0.0204600198138956!23293$GO:0050658!RNA transport!0.0204600198138956!23293$GO:0051236!establishment of RNA localization!0.0204600198138956!23293$GO:0050657!nucleic acid transport!0.0204600198138956!23293$GO:0006403!RNA localization!0.0204600198138956!23293$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0221611014011255!23293$GO:0043232!intracellular non-membrane-bound organelle!0.024713451545318!23293;1060$GO:0043228!non-membrane-bound organelle!0.024713451545318!23293;1060$GO:0030145!manganese ion binding!0.0265729373489249!23293$GO:0004519!endonuclease activity!0.0265729373489249!23293$GO:0006913!nucleocytoplasmic transport!0.0265729373489249!23293$GO:0051169!nuclear transport!0.0265729373489249!23293$GO:0003677!DNA binding!0.0298832650009259!23293;1060$GO:0032991!macromolecular complex!0.0355109874751774!23293;1060$GO:0004518!nuclease activity!0.0367296420604185!23293$GO:0044446!intracellular organelle part!0.0367296420604185!23293;1060$GO:0044422!organelle part!0.0367296420604185!23293;1060$GO:0016311!dephosphorylation!0.0396731410028892!23293$GO:0016071!mRNA metabolic 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095.1;0,MA0098.1;0,MA0100.1;3.60951,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;1.35563,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;1.31729,MA0145.1;0.752137,MA0146.1;1.70974,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.9924,MA0035.2;0.894194,MA0039.2;0.757898,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,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;1.43223,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3615_CD4_CD8_Natural_Mast_CD19_granulocyte_Basophils
|gostat_on_coexpression_clusters=GO:0044427!chromosomal part!0.00640195440246109!23293;1060$GO:0005694!chromosome!0.00640195440246109!23293;1060$GO:0005697!telomerase holoenzyme complex!0.00640195440246109!23293$GO:0035303!regulation of dephosphorylation!0.00640195440246109!23293$GO:0042162!telomeric DNA binding!0.0122082852453962!23293$GO:0000184!mRNA catabolic process, nonsense-mediated decay!0.0122082852453962!23293$GO:0006406!mRNA export from nucleus!0.0122082852453962!23293$GO:0032200!telomere organization and biogenesis!0.0122082852453962!23293$GO:0006402!mRNA catabolic process!0.0122082852453962!23293$GO:0000723!telomere maintenance!0.0122082852453962!23293$GO:0006405!RNA export from nucleus!0.0122082852453962!23293$GO:0000781!chromosome, telomeric region!0.0122082852453962!23293$GO:0000776!kinetochore!0.0122082852453962!1060$GO:0051168!nuclear export!0.0156966496204888!23293$GO:0006401!RNA catabolic process!0.0156966496204888!23293$GO:0051174!regulation of phosphorus metabolic process!0.0204600198138956!23293$GO:0019220!regulation of phosphate metabolic process!0.0204600198138956!23293$GO:0000775!chromosome, pericentric region!0.0204600198138956!1060$GO:0051028!mRNA transport!0.0204600198138956!23293$GO:0050658!RNA transport!0.0204600198138956!23293$GO:0051236!establishment of RNA localization!0.0204600198138956!23293$GO:0050657!nucleic acid transport!0.0204600198138956!23293$GO:0006403!RNA localization!0.0204600198138956!23293$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0221611014011255!23293$GO:0043232!intracellular non-membrane-bound organelle!0.024713451545318!23293;1060$GO:0043228!non-membrane-bound organelle!0.024713451545318!23293;1060$GO:0030145!manganese ion binding!0.0265729373489249!23293$GO:0004519!endonuclease activity!0.0265729373489249!23293$GO:0006913!nucleocytoplasmic transport!0.0265729373489249!23293$GO:0051169!nuclear transport!0.0265729373489249!23293$GO:0003677!DNA binding!0.0298832650009259!23293;1060$GO:0032991!macromolecular complex!0.0355109874751774!23293;1060$GO:0004518!nuclease activity!0.0367296420604185!23293$GO:0044446!intracellular organelle part!0.0367296420604185!23293;1060$GO:0044422!organelle part!0.0367296420604185!23293;1060$GO:0016311!dephosphorylation!0.0396731410028892!23293$GO:0016071!mRNA metabolic process!0.0471050325502772!23293
|id=C3615
}}

Latest revision as of 12:29, 17 September 2013


Full id: C3615_CD4_CD8_Natural_Mast_CD19_granulocyte_Basophils



Phase1 CAGE Peaks

Hg19::chr17:2207011..2207061,-p3@SMG6
Hg19::chr4:68411097..68411110,-p4@CENPC1
Hg19::chr4:68411152..68411174,-p2@CENPC1


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:0044427chromosomal part0.00640195440246109
GO:0005694chromosome0.00640195440246109
GO:0005697telomerase holoenzyme complex0.00640195440246109
GO:0035303regulation of dephosphorylation0.00640195440246109
GO:0042162telomeric DNA binding0.0122082852453962
GO:0000184mRNA catabolic process, nonsense-mediated decay0.0122082852453962
GO:0006406mRNA export from nucleus0.0122082852453962
GO:0032200telomere organization and biogenesis0.0122082852453962
GO:0006402mRNA catabolic process0.0122082852453962
GO:0000723telomere maintenance0.0122082852453962
GO:0006405RNA export from nucleus0.0122082852453962
GO:0000781chromosome, telomeric region0.0122082852453962
GO:0000776kinetochore0.0122082852453962
GO:0051168nuclear export0.0156966496204888
GO:0006401RNA catabolic process0.0156966496204888
GO:0051174regulation of phosphorus metabolic process0.0204600198138956
GO:0019220regulation of phosphate metabolic process0.0204600198138956
GO:0000775chromosome, pericentric region0.0204600198138956
GO:0051028mRNA transport0.0204600198138956
GO:0050658RNA transport0.0204600198138956
GO:0051236establishment of RNA localization0.0204600198138956
GO:0050657nucleic acid transport0.0204600198138956
GO:0006403RNA localization0.0204600198138956
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0221611014011255
GO:0043232intracellular non-membrane-bound organelle0.024713451545318
GO:0043228non-membrane-bound organelle0.024713451545318
GO:0030145manganese ion binding0.0265729373489249
GO:0004519endonuclease activity0.0265729373489249
GO:0006913nucleocytoplasmic transport0.0265729373489249
GO:0051169nuclear transport0.0265729373489249
GO:0003677DNA binding0.0298832650009259
GO:0032991macromolecular complex0.0355109874751774
GO:0004518nuclease activity0.0367296420604185
GO:0044446intracellular organelle part0.0367296420604185
GO:0044422organelle part0.0367296420604185
GO:0016311dephosphorylation0.0396731410028892
GO:0016071mRNA metabolic process0.0471050325502772



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 cell3.81e-53168
angioblastic mesenchymal cell3.81e-53168
hematopoietic cell3.72e-50177
hematopoietic oligopotent progenitor cell1.93e-48161
hematopoietic multipotent progenitor cell1.93e-48161
leukocyte4.20e-40136
hematopoietic lineage restricted progenitor cell2.66e-32120
nongranular leukocyte3.51e-32115
myeloid cell8.08e-25108
common myeloid progenitor8.08e-25108
lymphocyte3.60e-2253
common lymphoid progenitor3.60e-2253
lymphoid lineage restricted progenitor cell1.00e-2152
nucleate cell8.61e-2155
myeloid leukocyte1.51e-1472
granulocyte monocyte progenitor cell3.97e-1367
classical monocyte2.04e-1242
CD14-positive, CD16-negative classical monocyte2.04e-1242
T cell4.15e-1225
pro-T cell4.15e-1225
myeloid lineage restricted progenitor cell2.61e-1166
mature alpha-beta T cell2.69e-1118
alpha-beta T cell2.69e-1118
immature T cell2.69e-1118
mature T cell2.69e-1118
immature alpha-beta T cell2.69e-1118
macrophage dendritic cell progenitor2.17e-1061
monopoietic cell7.56e-1059
monocyte7.56e-1059
monoblast7.56e-1059
promonocyte7.56e-1059
defensive cell2.13e-0948
phagocyte2.13e-0948
mesenchymal cell4.17e-09354
lymphocyte of B lineage5.09e-0924
pro-B cell5.09e-0924
connective tissue cell4.70e-08361
motile cell1.51e-07386
CD8-positive, alpha-beta T cell3.31e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.04e-1598
blood island1.04e-1598
hemolymphoid system3.67e-15108
immune system2.17e-1193
bone marrow3.21e-1076
bone element5.38e-1082
connective tissue1.97e-08371
skeletal element7.99e-0890
Disease
Ontology termp-valuen
hematologic cancer1.94e-1651
immune system cancer1.94e-1651
leukemia1.68e-1439
myeloid leukemia1.88e-1231


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
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
MA0073.10.0185922
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
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
MA0100.13.60951
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
MA0114.11.35563
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
MA0144.11.31729
MA0145.10.752137
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
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
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
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
BRCA1#672213.45615376214920.007119807716084560.0296213838210634
E2F1#186934.907389214879320.008460985347239390.0324849955400461
E2F6#187635.017155731697390.00791769806886330.0321657254011986
EGR1#195834.988179094810140.008056488137383440.0320196196278328
ELF1#199734.258097958807540.01295179875054610.0461663109115455
FOXA2#3170216.42030916844350.004810682352105480.0225858779128588
GTF2B#2959221.29588662288280.002878180589911410.0155788703099123
IRF1#365937.63716375356390.002244692747297240.0127923969134005
MYC#460935.22228187160940.007020843755740150.0294158904403156
NFKB1#479035.488063424193840.006049381815655430.0269340234235085
NFYA#4800212.28372046655370.008516011403724430.0324682844154921
NFYB#4801211.17319550235760.01025467135054530.0381202214336927
NRF1#4899312.21027944771090.0005492172401020010.00470817527201945
PAX5#507936.669565531177830.003370290999677260.0172772700002598
SIN3A#2594235.408884726815140.006318961977991520.0276289906229363
YY1#752834.911170749853860.008441455341808260.0328900262802877
ZBTB33#10009221.10981668665410.002928597060603240.0156330052855784



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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