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Coexpression cluster:C468: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.685475,0.18095,0.666843,0.18689,0.0772548,0.185775,0.239567,0.0302452,0.121741,3.43113,0.165709,0.272066,0.40338,0.6536,0.0765993,0.0881735,0.416635,0.196076,0.0930871,0.68534,0.0985208,0.416615,1.02103,0.0748199,0.124129,0.289541,0.173284,0.179098,0.571039,0.509878,0.462061,0.448071,0.362042,0.21322,0.831295,1.09902,1.73767,1.04515,0.0504655,1.12756,0.21951,0.436576,0.0917928,0.0758747,1.53949,0.744956,0.240368,0.479472,0.0087826,0.27085,0.300624,1.28662,0.0936711,0.515129,0.653159,0.658597,0.08088,0.603257,0.0544304,1.77602,0.483605,0.679156,0.122235,1.01901,1.31042,0.364726,0.73513,1.08739,0.43915,0.930562,1.33665,0.130122,1.84609,0.651319,2.20591,2.56151,0.157868,0.379205,0.436366,0.120546,0.09736,0.392395,0.25519,0.301476,0.604277,3.67069,0.150398,0.490541,0.859503,1.18432,0.823081,0.579812,0.462581,0.166137,0.267495,0.406805,0.0917805,1.24896,0.867748,0.42824,0.190137,0.45769,0.494867,0.419744,0.935363,1.51367,1.04752,1.20938,0.391767,1.34949,0.340916,0.492438,0.0955593,0.171884,0.777703,0.47017,1.44897,0.460172,0.951991,0.0442476,0.64371,0.319278,0.183912,0.729005,0.882719,0.989505,1.2332,0.466912,0.683004,0.182525,0.580435,0.153507,0.696335,0.723221,0.835304,4.27923,0.147939,1.01671,0.795107,1.6331,1.23566,0.759951,0.236178,0.496668,0.938543,0.589128,0.343142,1.4753,0.139503,1.02762,1.02955,3.4703,0.58078,0.81624,0.241755,0.959994,0.308372,0.0706846,0.124164,2.32988,0.758809,0.564094,0.435692,1.18197,0.967734,0.708093,0.344454,0.238589,1.94244
|tfbs_overrepresentation_jaspar=MA0003.1;4.26182,MA0004.1;0.974673,MA0006.1;0.948059,MA0007.1;0.156885,MA0009.1;0.543169,MA0014.1;4.30893,MA0017.1;0.0964051,MA0019.1;0.757112,MA0024.1;0.450307,MA0025.1;0.665335,MA0027.1;2.11401,MA0028.1;1.00696,MA0029.1;0.467171,MA0030.1;0.457153,MA0031.1;0.401568,MA0038.1;0.678012,MA0040.1;0.472301,MA0041.1;0.181587,MA0042.1;0.160318,MA0043.1;0.543454,MA0046.1;0.533373,MA0048.1;0.211102,MA0050.1;0.160894,MA0051.1;0.670696,MA0052.1;0.475699,MA0055.1;1.77973,MA0056.1;0,MA0057.1;0.81762,MA0058.1;0.721539,MA0059.1;0.109562,MA0060.1;1.67182,MA0061.1;0.0956181,MA0063.1;0,MA0066.1;0.241938,MA0067.1;0.83875,MA0068.1;0.562572,MA0069.1;0.529912,MA0070.1;0.519883,MA0071.1;0.213282,MA0072.1;0.515863,MA0073.1;0.420952,MA0074.1;0.669394,MA0076.1;0.379988,MA0077.1;0.508982,MA0078.1;0.31524,MA0081.1;0.354412,MA0083.1;1.35561,MA0084.1;1.01907,MA0087.1;0.513678,MA0088.1;0.68602,MA0089.1;0,MA0090.1;0.402075,MA0091.1;0.170864,MA0092.1;0.146372,MA0093.1;0.959157,MA0095.1;0,MA0098.1;0,MA0100.1;0.252028,MA0101.1;0.272702,MA0103.1;0.0719484,MA0105.1;0.168486,MA0106.1;1.37512,MA0107.1;0.046982,MA0108.2;0.398967,MA0109.1;0,MA0111.1;0.136202,MA0113.1;0.285689,MA0114.1;0.17185,MA0115.1;0.766188,MA0116.1;0.40798,MA0117.1;0.577217,MA0119.1;1.65035,MA0122.1;0.600851,MA0124.1;0.727093,MA0125.1;0.648747,MA0130.1;0,MA0131.1;0.878923,MA0132.1;0,MA0133.1;0,MA0135.1;0.570637,MA0136.1;0.246897,MA0139.1;1.37627,MA0140.1;0.606998,MA0141.1;0.351584,MA0142.1;0.374765,MA0143.1;0.285827,MA0144.1;0.356992,MA0145.1;2.46877,MA0146.1;1.88618,MA0147.1;0.186237,MA0148.1;0.185927,MA0149.1;0.204488,MA0062.2;1.42844,MA0035.2;0.605801,MA0039.2;5.80456,MA0138.2;0.316226,MA0002.2;0.0261526,MA0137.2;0.0876366,MA0104.2;0.28985,MA0047.2;0.263601,MA0112.2;0.504966,MA0065.2;0.560145,MA0150.1;0.124469,MA0151.1;0,MA0152.1;0.216094,MA0153.1;0.633172,MA0154.1;0.0728322,MA0155.1;1.2055,MA0156.1;0.0888107,MA0157.1;0.352016,MA0158.1;0,MA0159.1;0.417407,MA0160.1;0.196462,MA0161.1;0,MA0162.1;3.99333,MA0163.1;4.03174,MA0164.1;0.295453,MA0080.2;0.268297,MA0018.2;0.752684,MA0099.2;0.216352,MA0079.2;5.7644,MA0102.2;1.05522,MA0258.1;0.0364681,MA0259.1;0.435255,MA0442.1;0
}}
}}

Revision as of 19:11, 22 January 2013


Full id: C468_Neutrophils_Eosinophils_cerebellum_occipital_Whole_temporal_parietal



Phase1 CAGE Peaks

Hg19::chr11:74459876..74459930,+p1@RNF169
Hg19::chr12:76953574..76953598,-p3@OSBPL8
Hg19::chr14:52327421..52327458,+p3@GNG2
Hg19::chr17:11924129..11924200,+p1@MAP2K4
Hg19::chr17:47439568..47439641,-p2@ZNF652
Hg19::chr1:89149914..89149995,+p1@PKN2
Hg19::chr20:60813535..60813592,+p2@OSBPL2
Hg19::chr2:139259324..139259389,+p1@SPOPL
Hg19::chr2:160472952..160473077,-p1@BAZ2B
Hg19::chr2:201936328..201936416,-p1@FAM126B
Hg19::chr2:24714108..24714152,+p@chr2:24714108..24714152
+
Hg19::chr2:86850949..86851023,-p1@RNF103
Hg19::chr3:184529948..184529990,+p1@VPS8
Hg19::chr4:6784401..6784510,+p1@KIAA0232
Hg19::chr4:89513578..89513670,+p1@HERC3
Hg19::chr5:112043186..112043225,+p2@APC
Hg19::chr6:137113489..137113569,-p1@MAP3K5
Hg19::chr6:42531690..42531718,+p2@UBR2
Hg19::chr7:30634347..30634400,-p1@uc003tbj.2
p1@uc003tbl.3
p1@uc010kvv.2
Hg19::chr8:52811714..52811731,-p3@PCMTD1
Hg19::chrX:80065146..80065250,-p1@BRWD3


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:0006464protein modification process0.0195237347183443
GO:0043412biopolymer modification0.0195237347183443
GO:0051983regulation of chromosome segregation0.0195237347183443
GO:0051988regulation of attachment of spindle microtubules to kinetochore0.0195237347183443
GO:0008608attachment of spindle microtubules to kinetochore0.0195237347183443
GO:0007254JNK cascade0.0195237347183443
GO:0031098stress-activated protein kinase signaling pathway0.0195237347183443
GO:0043687post-translational protein modification0.0216695468435289



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
leukocyte1.99e-28136
hematopoietic stem cell1.08e-23168
angioblastic mesenchymal cell1.08e-23168
hematopoietic lineage restricted progenitor cell3.94e-23120
myeloid leukocyte1.18e-2272
hematopoietic oligopotent progenitor cell9.51e-22161
hematopoietic multipotent progenitor cell9.51e-22161
nongranular leukocyte4.08e-21115
granulocyte monocyte progenitor cell1.61e-1967
hematopoietic cell1.68e-19177
myeloid lineage restricted progenitor cell6.12e-1966
macrophage dendritic cell progenitor2.42e-1761
myeloid cell4.06e-17108
common myeloid progenitor4.06e-17108
monopoietic cell9.35e-1759
monocyte9.35e-1759
monoblast9.35e-1759
promonocyte9.35e-1759
defensive cell1.95e-1648
phagocyte1.95e-1648
classical monocyte4.27e-1642
CD14-positive, CD16-negative classical monocyte4.27e-1642
mature alpha-beta T cell9.26e-0718
alpha-beta T cell9.26e-0718
immature T cell9.26e-0718
mature T cell9.26e-0718
immature alpha-beta T cell9.26e-0718
Uber Anatomy
Ontology termp-valuen
adult organism1.58e-44114
neural tube1.13e-2456
neural rod1.13e-2456
future spinal cord1.13e-2456
neural keel1.13e-2456
regional part of nervous system3.41e-2353
regional part of brain3.41e-2353
regional part of forebrain3.36e-2241
forebrain3.36e-2241
anterior neural tube3.36e-2241
future forebrain3.36e-2241
central nervous system1.17e-2081
hematopoietic system1.49e-2098
blood island1.49e-2098
brain5.19e-2068
future brain5.19e-2068
nervous system1.18e-1989
telencephalon1.51e-1834
brain grey matter2.19e-1834
gray matter2.19e-1834
cerebral hemisphere1.90e-1732
hemolymphoid system1.97e-17108
regional part of telencephalon2.31e-1732
bone marrow7.23e-1576
regional part of cerebral cortex1.07e-1422
neocortex1.81e-1320
bone element1.93e-1382
cerebral cortex1.94e-1325
pallium1.94e-1325
neurectoderm2.99e-1386
neural plate3.40e-1382
presumptive neural plate3.40e-1382
immune system5.18e-1393
skeletal element4.64e-1190
skeletal system1.47e-10100
pre-chordal neural plate1.51e-1061
ecto-epithelium1.27e-07104
ectoderm-derived structure5.06e-07171
ectoderm5.06e-07171
presumptive ectoderm5.06e-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)
MA0003.14.26182
MA0004.10.974673
MA0006.10.948059
MA0007.10.156885
MA0009.10.543169
MA0014.14.30893
MA0017.10.0964051
MA0019.10.757112
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.11.00696
MA0029.10.467171
MA0030.10.457153
MA0031.10.401568
MA0038.10.678012
MA0040.10.472301
MA0041.10.181587
MA0042.10.160318
MA0043.10.543454
MA0046.10.533373
MA0048.10.211102
MA0050.10.160894
MA0051.10.670696
MA0052.10.475699
MA0055.11.77973
MA0056.10
MA0057.10.81762
MA0058.10.721539
MA0059.10.109562
MA0060.11.67182
MA0061.10.0956181
MA0063.10
MA0066.10.241938
MA0067.10.83875
MA0068.10.562572
MA0069.10.529912
MA0070.10.519883
MA0071.10.213282
MA0072.10.515863
MA0073.10.420952
MA0074.10.669394
MA0076.10.379988
MA0077.10.508982
MA0078.10.31524
MA0081.10.354412
MA0083.11.35561
MA0084.11.01907
MA0087.10.513678
MA0088.10.68602
MA0089.10
MA0090.10.402075
MA0091.10.170864
MA0092.10.146372
MA0093.10.959157
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.272702
MA0103.10.0719484
MA0105.10.168486
MA0106.11.37512
MA0107.10.046982
MA0108.20.398967
MA0109.10
MA0111.10.136202
MA0113.10.285689
MA0114.10.17185
MA0115.10.766188
MA0116.10.40798
MA0117.10.577217
MA0119.11.65035
MA0122.10.600851
MA0124.10.727093
MA0125.10.648747
MA0130.10
MA0131.10.878923
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.246897
MA0139.11.37627
MA0140.10.606998
MA0141.10.351584
MA0142.10.374765
MA0143.10.285827
MA0144.10.356992
MA0145.12.46877
MA0146.11.88618
MA0147.10.186237
MA0148.10.185927
MA0149.10.204488
MA0062.21.42844
MA0035.20.605801
MA0039.25.80456
MA0138.20.316226
MA0002.20.0261526
MA0137.20.0876366
MA0104.20.28985
MA0047.20.263601
MA0112.20.504966
MA0065.20.560145
MA0150.10.124469
MA0151.10
MA0152.10.216094
MA0153.10.633172
MA0154.10.0728322
MA0155.11.2055
MA0156.10.0888107
MA0157.10.352016
MA0158.10
MA0159.10.417407
MA0160.10.196462
MA0161.10
MA0162.13.99333
MA0163.14.03174
MA0164.10.295453
MA0080.20.268297
MA0018.20.752684
MA0099.20.216352
MA0079.25.7644
MA0102.21.05522
MA0258.10.0364681
MA0259.10.435255
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#46766.418049864573930.0002361560373475430.00257317687892958
BCLAF1#977466.18647074574910.0002880257333882330.00306137996838323
BHLHE40#855336.410259078139630.01089557130462060.0401752072971074
BRCA1#67254.805769200767560.003112207706263310.0163605909616165
CCNT2#905133.922410500024492.16439215182906e-067.82711052440703e-05
CHD2#110683.940580127282610.0004867168088467780.0043528187017596
CTCF#10664123.063003641757169.61865604962896e-050.00136973386851268
CTCFL#14069065.641849816849820.000472078892849080.00433360705724401
E2F1#1869133.037907609211013.99747315883528e-050.000733987516236986
E2F4#187474.222686771761480.0008214886927013180.00625696160859342
E2F6#1876122.866946132398510.0001873551368669690.0022655069050885
EGR1#1958153.562985067721535.29066604052795e-072.46895384542761e-05
ELF1#1997193.852564819873491.40187937768485e-101.49094582816729e-08
ELK4#200553.865638490111430.007841746422441410.0322054327413826
GABPB1#2553124.038676477818385.38690292930369e-060.000164551844116276
GTF2F1#296263.639903107645040.00451650251172950.0213535086384118
HDAC2#306663.833034353321790.003492483739868060.0177373813123945
HEY1#23462183.462952322662047.24417577880214e-095.62508902722912e-07
HMGN3#9324114.284001188421749.84651420879756e-060.000258252159079008
IRF1#3659155.455116966831361.40708023377392e-091.26032635107302e-07
IRF3#366136.711707458784230.009620809191356820.0362059560080756
JUND#3727103.330792353271920.0002747494982675180.00292891322339097
MAX#4149113.379910028527549.5149658187134e-050.00136221180965128
MXI1#460183.794884430003540.0006282445088767760.00516965240014037
MYC#4609133.232841158615341.98900354493168e-050.00044160191587823
NFKB1#4790123.136036242396487.56729836316575e-050.00117101951955944
PAX5#5079113.493581944902676.97253825644776e-050.00110535052059069
POLR2A#5430212.147453176558071.06914340939766e-076.24149069502978e-06
POU2F2#5452104.336249551305962.84162272309111e-050.000599184808352337
RFX5#599363.442260236341460.005942267186721130.0266502530473641
SIN3A#25942133.348357211837941.33646012272453e-050.000326194341568654
SP1#6667133.527569424563417.37205723419176e-060.000211577434867203
SRF#672285.256067909397266.54168363195151e-050.00106153961596859
TAF1#6872203.183853605471714.92884944828003e-104.77961102626664e-08
TAF7#687984.355455011399590.0002448846036019360.00266328263205067
TBP#6908193.353744907372921.79157243688477e-091.55665585470723e-07
TFAP2A#702053.933008184058320.007297224656068850.0301851570760129
TFAP2C#702263.088351031388640.01002037961740120.0375702181605372
USF1#739182.423428296079220.01102567951586520.04055901317169
YY1#7528163.741844380841036.13111176653469e-083.79790736527353e-06
ZBTB7A#5134193.150818274803960.0009903620425291610.00710826894094585
ZEB1#693575.629477339181290.0001413376962256970.00184238238343929
ZZZ3#26009222.80125832716510.00347123499089870.0176320369249778



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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