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Coexpression cluster:C4133: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;1.5435,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;2.15619,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;5.37342,MA0058.1;0.716037,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;3.76647,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;18.7134,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;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;6.40038,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.195278,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;1.39232,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;0.149099,MA0163.1;2.48891,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;19.494,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:51, 22 January 2013


Full id: C4133_occipital_parietal_temporal_optic_CD14_rectum_ovary



Phase1 CAGE Peaks

Hg19::chr2:145277792..145277808,-p15@ZEB2
Hg19::chr2:145277820..145277831,-p18@ZEB2
Hg19::chr2:145277833..145277845,-p16@ZEB2


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

No GOStat results

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 lineage restricted progenitor cell3.39e-3066
myeloid leukocyte5.55e-2972
monopoietic cell1.77e-2859
monocyte1.77e-2859
monoblast1.77e-2859
promonocyte1.77e-2859
granulocyte monocyte progenitor cell2.02e-2867
macrophage dendritic cell progenitor9.91e-2761
defensive cell5.35e-2548
phagocyte5.35e-2548
classical monocyte6.45e-2342
CD14-positive, CD16-negative classical monocyte6.45e-2342
myeloid cell8.03e-22108
common myeloid progenitor8.03e-22108
stuff accumulating cell1.79e-1787
leukocyte2.02e-09136
hematopoietic lineage restricted progenitor cell4.41e-09120
hematopoietic oligopotent progenitor cell9.10e-09161
hematopoietic multipotent progenitor cell9.10e-09161
hematopoietic stem cell9.28e-09168
angioblastic mesenchymal cell9.28e-09168
nongranular leukocyte1.02e-08115
hematopoietic cell1.90e-07177
Uber Anatomy
Ontology termp-valuen
adult organism1.32e-31114
bone marrow2.63e-2476
hematopoietic system1.47e-2398
blood island1.47e-2398
bone element1.49e-2382
neural tube9.16e-2256
neural rod9.16e-2256
future spinal cord9.16e-2256
neural keel9.16e-2256
skeletal system6.43e-21100
skeletal element2.47e-2090
hemolymphoid system4.27e-20108
regional part of nervous system1.45e-1953
regional part of brain1.45e-1953
immune system6.08e-1993
regional part of forebrain6.26e-1841
forebrain6.26e-1841
anterior neural tube6.26e-1841
future forebrain6.26e-1841
central nervous system1.36e-1781
telencephalon4.27e-1734
brain grey matter7.60e-1734
gray matter7.60e-1734
nervous system4.81e-1689
regional part of telencephalon1.31e-1532
cerebral hemisphere1.33e-1532
brain1.38e-1568
future brain1.38e-1568
neurectoderm3.76e-1586
neural plate3.09e-1482
presumptive neural plate3.09e-1482
neocortex1.59e-1320
regional part of cerebral cortex4.68e-1322
cerebral cortex3.78e-1225
pallium3.78e-1225
pre-chordal neural plate1.03e-1161
musculoskeletal system3.19e-11167
structure with developmental contribution from neural crest1.10e-09132
ecto-epithelium4.15e-09104
organ1.35e-08503
germ layer3.35e-08560
germ layer / neural crest3.35e-08560
embryonic tissue3.35e-08560
presumptive structure3.35e-08560
germ layer / neural crest derived structure3.35e-08560
epiblast (generic)3.35e-08560
tissue4.42e-08773
embryonic structure4.52e-08564
developing anatomical structure3.25e-07581
embryo4.26e-07592
ectoderm-derived structure5.82e-07171
ectoderm5.82e-07171
presumptive ectoderm5.82e-07171


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)
MA0003.10.178364
MA0004.10.826076
MA0006.11.5435
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
MA0051.12.15619
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.15.37342
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.13.76647
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.118.7134
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
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.16.40038
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
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
MA0162.10.149099
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.219.494
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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139356656981578
CCNT2#90536.336201576962630.003930750035764890.0190436332970844
CTCF#1066435.360256373075030.0064925092527670.0280044262937155
CTCFL#140690319.74647435897440.0001298372005551160.00172038408890837
E2F6#187635.017155731697390.00791769806886330.0323039483011959
ELF1#199734.258097958807540.01295179875054610.0463355225467846
EP300#203336.77394172622320.003216880500103790.0167740667307574
GATA2#2624312.7449317335540.0004829527704283790.00437535603667328
GTF2B#2959331.94382993432423.06634405746243e-050.000628672766033214
IRF1#365937.63716375356390.002244692747297240.0128358227023093
JUND#372736.994663941871030.002921845042734990.0157061389890473
RAD21#5885310.35503389545630.0009004912073565420.00665438344336729
REST#597839.650028716128020.001112636247114590.0076904445408604
SIRT6#515483153.6384039900252.75057764221434e-071.40062203010836e-05
TRIM28#10155318.59052504526250.0001555969297255280.00197405098926195
USF1#739136.361499277207960.00388404057290560.0190712418144658
YY1#752834.911170749853860.008441455341808260.0330033000577664
ZBTB7A#5134137.35190930787590.002516255860282270.0140524702311117



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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