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Coexpression cluster:C3145: 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;0.758317,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;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;1.59304,MA0058.1;1.70328,MA0059.1;0.714521,MA0060.1;0.492218,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;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;1.55117,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;1.31729,MA0145.1;0.752137,MA0146.1;2.3244,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;1.60005,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;0.838867,MA0155.1;1.31345,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;2.05956,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.90288,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:10, 22 January 2013


Full id: C3145_Neutrophils_left_CD14_heart_Eosinophils_breast_mature



Phase1 CAGE Peaks

Hg19::chr11:33278811..33279020,+p1@HIPK3
Hg19::chr11:33279850..33279931,+p2@HIPK3
Hg19::chr4:15656923..15657009,-p1@FBXL5


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:0043508negative regulation of JNK activity0.00571041708603294
GO:0018107peptidyl-threonine phosphorylation0.00571041708603294
GO:0018210peptidyl-threonine modification0.00571041708603294
GO:0018209peptidyl-serine modification0.0114196574596843
GO:0018105peptidyl-serine phosphorylation0.0114196574596843
GO:0043407negative regulation of MAP kinase activity0.020387742737772
GO:0043506regulation of JNK activity0.020387742737772
GO:0006469negative regulation of protein kinase activity0.0330794695081121
GO:0033673negative regulation of kinase activity0.0330794695081121
GO:0051348negative regulation of transferase activity0.0330794695081121
GO:0016567protein ubiquitination0.0330794695081121
GO:0043687post-translational protein modification0.0330794695081121
GO:0032446protein modification by small protein conjugation0.0330794695081121
GO:0000151ubiquitin ligase complex0.0330794695081121
GO:0043086negative regulation of catalytic activity0.0330794695081121
GO:0043405regulation of MAP kinase activity0.0331478301936655
GO:0006464protein modification process0.0361365010347462
GO:0043412biopolymer modification0.0363031783622391
GO:0018193peptidyl-amino acid modification0.0363031783622391
GO:0004842ubiquitin-protein ligase activity0.044017486364433
GO:0008639small protein conjugating enzyme activity0.044017486364433
GO:0006916anti-apoptosis0.044017486364433



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
myeloid leukocyte8.58e-3272
granulocyte monocyte progenitor cell2.10e-2867
macrophage dendritic cell progenitor1.21e-2661
monopoietic cell5.78e-2659
monocyte5.78e-2659
monoblast5.78e-2659
promonocyte5.78e-2659
defensive cell1.81e-2548
phagocyte1.81e-2548
classical monocyte3.20e-2542
CD14-positive, CD16-negative classical monocyte3.20e-2542
myeloid lineage restricted progenitor cell4.26e-2566
leukocyte1.25e-21136
hematopoietic lineage restricted progenitor cell9.12e-18120
nongranular leukocyte3.07e-17115
myeloid cell6.67e-17108
common myeloid progenitor6.67e-17108
hematopoietic stem cell7.29e-14168
angioblastic mesenchymal cell7.29e-14168
hematopoietic oligopotent progenitor cell2.98e-13161
hematopoietic multipotent progenitor cell2.98e-13161
stuff accumulating cell6.07e-1287
hematopoietic cell8.17e-12177
Uber Anatomy
Ontology termp-valuen
adult organism1.18e-40114
hematopoietic system7.26e-2898
blood island7.26e-2898
hemolymphoid system3.96e-25108
bone marrow1.34e-2376
immune system1.40e-2093
bone element1.59e-2082
skeletal element5.49e-2090
skeletal system1.39e-17100
neural tube3.09e-1156
neural rod3.09e-1156
future spinal cord3.09e-1156
neural keel3.09e-1156
regional part of nervous system3.36e-1053
regional part of brain3.36e-1053
regional part of forebrain1.20e-0941
forebrain1.20e-0941
anterior neural tube1.20e-0941
future forebrain1.20e-0941
central nervous system4.10e-0881
brain5.26e-0868
future brain5.26e-0868
musculoskeletal system6.34e-08167
brain grey matter1.37e-0734
gray matter1.37e-0734
telencephalon2.74e-0734
nervous system4.76e-0789
regional part of telencephalon6.83e-0732


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
MA0014.10.758317
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.11.70328
MA0059.10.714521
MA0060.10.492218
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
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
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
MA0144.11.31729
MA0145.10.752137
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
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#90536.336201576962630.003930750035764890.0189216262437891
E2F1#186934.907389214879320.008460985347239390.0323731260507157
EGR1#195834.988179094810140.008056488137383440.0319139603481961
HMGN3#932438.178547723350590.001827766942164210.0108343351877342
PAX5#507936.669565531177830.003370290999677260.0172341275810465
TFAP2A#7020316.5186343730450.0002218033880766340.00247409206956484
YY1#752834.911170749853860.008441455341808260.0328031386531892



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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