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Coexpression cluster:C3394: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;3.22681,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.24048,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;0.557638,MA0056.1;0,MA0057.1;0.886807,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;2.26659,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;0.715722,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;0.846801,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;1.12079,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;0.707589,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;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;0.711948,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;6.30148,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:20, 22 January 2013


Full id: C3394_Eosinophils_CD14_cerebellum_pineal_Neutrophils_CD4_Peripheral



Phase1 CAGE Peaks

Hg19::chr14:102414651..102414721,+p@chr14:102414651..102414721
+
Hg19::chr2:157198916..157198978,-p2@NR4A2
Hg19::chr5:98264867..98264903,+p1@ENST00000513175


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:0042053regulation of dopamine metabolic process0.00500412104085718
GO:0042069regulation of catecholamine metabolic process0.00500412104085718
GO:0042417dopamine metabolic process0.00917422190823815
GO:0006584catecholamine metabolic process0.0133443227756191
GO:0018958phenol metabolic process0.0133443227756191
GO:0042133neurotransmitter metabolic process0.0133443227756191
GO:0006576biogenic amine metabolic process0.0243950900741787
GO:0001505regulation of neurotransmitter levels0.0243950900741787
GO:0006575amino acid derivative metabolic process0.0250206052042859
GO:0003707steroid hormone receptor activity0.0292741080890145
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0316169465763249
GO:0004879ligand-dependent nuclear receptor activity0.0319012716354645
GO:0006725aromatic compound metabolic process0.0352213134798794
GO:0030182neuron differentiation0.0362798775462145
GO:0045893positive regulation of transcription, DNA-dependent0.0362798775462145
GO:0048699generation of neurons0.0362798775462145
GO:0022008neurogenesis0.0362798775462145
GO:0045941positive regulation of transcription0.0362798775462145
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0362798775462145
GO:0007268synaptic transmission0.0362798775462145
GO:0019226transmission of nerve impulse0.0393180938924492
GO:0031325positive regulation of cellular metabolic process0.0415114586343834
GO:0009893positive regulation of metabolic process0.042535028847286
GO:0006357regulation of transcription from RNA polymerase II promoter0.0440988166725538
GO:0006066alcohol metabolic process0.0445366772636289



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
leukocyte9.99e-28136
classical monocyte1.51e-2442
CD14-positive, CD16-negative classical monocyte1.51e-2442
myeloid leukocyte2.23e-2472
defensive cell9.21e-2448
phagocyte9.21e-2448
hematopoietic lineage restricted progenitor cell3.98e-23120
nongranular leukocyte1.07e-21115
myeloid lineage restricted progenitor cell5.16e-2066
granulocyte monocyte progenitor cell3.90e-1967
hematopoietic stem cell5.82e-19168
angioblastic mesenchymal cell5.82e-19168
hematopoietic cell1.44e-18177
macrophage dendritic cell progenitor1.90e-1861
monopoietic cell4.27e-1859
monocyte4.27e-1859
monoblast4.27e-1859
promonocyte4.27e-1859
hematopoietic oligopotent progenitor cell4.53e-17161
hematopoietic multipotent progenitor cell4.53e-17161
myeloid cell8.16e-13108
common myeloid progenitor8.16e-13108
stuff accumulating cell1.37e-0987
Uber Anatomy
Ontology termp-valuen
adult organism3.82e-26114
hematopoietic system9.12e-2198
blood island9.12e-2198
neural tube3.89e-1956
neural rod3.89e-1956
future spinal cord3.89e-1956
neural keel3.89e-1956
bone marrow5.35e-1976
regional part of nervous system7.98e-1853
regional part of brain7.98e-1853
hemolymphoid system1.10e-17108
bone element1.60e-1782
skeletal element5.09e-1590
regional part of forebrain6.99e-1541
forebrain6.99e-1541
anterior neural tube6.99e-1541
future forebrain6.99e-1541
immune system2.13e-1493
skeletal system2.44e-13100
brain5.58e-1268
future brain5.58e-1268
brain grey matter8.92e-1234
gray matter8.92e-1234
telencephalon1.57e-1134
neural plate2.02e-1182
presumptive neural plate2.02e-1182
regional part of telencephalon5.73e-1132
cerebral hemisphere9.69e-1132
neurectoderm1.97e-1086
central nervous system2.47e-1081
regional part of cerebral cortex1.39e-0822
nervous system1.96e-0889
cerebral cortex3.58e-0825
pallium3.58e-0825
neocortex7.74e-0820
pre-chordal neural plate1.46e-0761


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0055.10.557638
MA0056.10
MA0057.10.886807
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
MA0073.12.26659
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.846801
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
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
MA0155.10.711948
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
MA0079.26.30148
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
CCNT2#90536.336201576962630.003930750035764890.0189557003733319
E2F1#186934.907389214879320.008460985347239390.0324253944180366
E2F6#187635.017155731697390.00791769806886330.0321170027037718
ELF1#199734.258097958807540.01295179875054610.0460908037927042
GTF2B#2959221.29588662288280.002878180589911410.0155756413611978
HMGN3#932438.178547723350590.001827766942164210.0108491134795504
HNF4A#3172215.42152690863580.005444210486686610.0246729398576291
MEF2A#4205212.4954872730960.008235029478029740.032479540923563
NRF1#4899312.21027944771090.0005492172401020010.00470161469991909
PAX5#507936.669565531177830.003370290999677260.0172577869050448
SREBF2#67211145.6477541371160.006850215514569990.0290447246722221
TAF7#6879311.43306940492390.0006690181981945830.00541556282756503
TFAP2A#7020211.01242291536330.01054990655215560.0390011571413608
YY1#752834.911170749853860.008441455341808260.0328508087507215



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:C3394&oldid=2571905"