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Coexpression cluster:C4300: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,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;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;1.23283,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,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;1.15986,MA0138.2;1.04628,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;1.76247,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;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.0373086,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:58, 22 January 2013


Full id: C4300_Basophils_Eosinophils_Mast_CD14_CD34_CD4_CD8



Phase1 CAGE Peaks

Hg19::chr3:16306114..16306133,-p5@DPH3
Hg19::chr3:53925835..53925860,-p2@ENST00000487571
Hg19::chr3:53925863..53925933,-p1@ENST00000485414
p1@ENST00000487571
p1@ENST00000488746


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:0017182peptidyl-diphthamide metabolic process0.00147180030613446
GO:0017183peptidyl-diphthamide biosynthetic process from peptidyl-histidine0.00147180030613446
GO:0051099positive regulation of binding0.00220770045920169
GO:0050709negative regulation of protein secretion0.00220770045920169
GO:0018202peptidyl-histidine modification0.00323796067349582
GO:0051048negative regulation of secretion0.00417010086738098
GO:0050708regulation of protein secretion0.00515130107147062
GO:0051098regulation of binding0.00515130107147062
GO:0009306protein secretion0.00868362180619334
GO:0051046regulation of secretion0.00868362180619334
GO:0018193peptidyl-amino acid modification0.0161898033674791
GO:0032940secretion by cell0.036427057576828
GO:0046903secretion0.0434747167350488



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
leukocyte1.37e-36136
hematopoietic lineage restricted progenitor cell3.67e-30120
nongranular leukocyte7.55e-27115
hematopoietic stem cell4.75e-23168
angioblastic mesenchymal cell4.75e-23168
hematopoietic cell1.00e-22177
myeloid leukocyte1.04e-2272
hematopoietic oligopotent progenitor cell6.12e-21161
hematopoietic multipotent progenitor cell6.12e-21161
classical monocyte1.07e-2042
CD14-positive, CD16-negative classical monocyte1.07e-2042
myeloid lineage restricted progenitor cell3.48e-1966
defensive cell5.59e-1948
phagocyte5.59e-1948
granulocyte monocyte progenitor cell4.18e-1867
macrophage dendritic cell progenitor1.49e-1661
monopoietic cell1.58e-1559
monocyte1.58e-1559
monoblast1.58e-1559
promonocyte1.58e-1559
nucleate cell3.57e-1155
myeloid cell4.17e-11108
common myeloid progenitor4.17e-11108
lymphocyte3.01e-1053
common lymphoid progenitor3.01e-1053
lymphoid lineage restricted progenitor cell3.66e-1052
stuff accumulating cell4.53e-0987
mesenchymal cell5.24e-09354
connective tissue cell6.12e-08361
mature alpha-beta T cell2.39e-0718
alpha-beta T cell2.39e-0718
immature T cell2.39e-0718
mature T cell2.39e-0718
immature alpha-beta T cell2.39e-0718
motile cell5.89e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.56e-2398
blood island4.56e-2398
hemolymphoid system2.35e-18108
bone marrow9.85e-1876
bone element3.38e-1682
adult organism4.88e-15114
skeletal element4.30e-1490
skeletal system1.42e-12100
immune system4.46e-1293
blood4.12e-0915
haemolymphatic fluid4.12e-0915
organism substance4.12e-0915
neural tube1.51e-0756
neural rod1.51e-0756
future spinal cord1.51e-0756
neural keel1.51e-0756
regional part of nervous system5.57e-0753
regional part of brain5.57e-0753
connective tissue6.68e-07371


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
MA0028.10.658629
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
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
MA0039.21.15986
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
ATF3#467322.46317452600878.81932387510763e-050.00129894424790913
BCLAF1#9774214.43509840674790.006201147435546130.0273936907630912
BRCA1#672213.45615376214920.007119807716084560.0296367316883282
CCNT2#90536.336201576962630.003930750035764890.0190604328621622
E2F1#186934.907389214879320.008460985347239390.0326602915686108
E2F6#187635.017155731697390.00791769806886330.0323405869847868
EGR1#195834.988179094810140.008056488137383440.032161591796506
ELF1#199734.258097958807540.01295179875054610.0463768268834053
ELK4#2005316.2356816584680.0002336043955745990.00256113893233419
GABPB1#255337.067683836182170.002832212825417420.0154542045597581
GATA1#2623313.56030814380040.0004009615963782630.00388748868957941
IRF1#365937.63716375356390.002244692747297240.0128456693608206
JUN#3725312.51282919233630.0005103313992726250.00445341753080161
MAFF#23764237.54357099329680.0009344774015560320.0067709092091793
MAFK#7975218.06715542521990.003983674744936810.0191155987450703
NANOG#79923219.49651898734180.003427255648501020.0174553375925972
NFE2#4778251.4695071010860.0004987653528392110.00440698432192677
NFKB1#479035.488063424193840.006049381815655430.027028508553807
NFYA#4800212.28372046655370.008516011403724430.0324872599259808
NFYB#4801211.17319550235760.01025467135054530.0381473774240284
PAX5#507936.669565531177830.003370290999677260.017336837990213
SETDB1#9869226.8800174520070.001814468907964410.010897143086768
SIN3A#2594235.408884726815140.006318961977991520.0277638228868093
SIX5#147912317.0867153554590.0002004060546325010.00240107926348099
SMARCB1#6598212.16847718743830.008675002221921740.033003371596069
SP1#666735.69838137814090.005403962701712170.024727675280587
SRF#6722313.79717826216780.0003806615025800190.00375835759765122
THAP1#55145331.36914460285133.23800758564397e-050.000648340249687635
YY1#752834.911170749853860.008441455341808260.0330404060429154



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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