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Coexpression cluster:C867: Difference between revisions

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{{Coexpression_clusters
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,0.226979,0.491955,0.287253,0.152349,0.152802,0.38832,0.00201112,0.117262,0.152699,0.321649,0.597602,0.50945,0.46408,0.190581,0.467691,0.22458,0.266409,0.180355,0.0588981,0.179632,0.282128,0.186072,0.211757,0.338622,0.29306,0.126579,0.187708,0.245457,0.106235,0.352719,0.496388,0.650742,0.637062,0.721601,0.367773,0.599943,0.222752,0.488202,0.538989,0.654598,0.584019,0.443905,0.632399,0.601983,0.345488,0.408688,0.499886,0.486539,0.637365,0.554869,0.330055,0.308763,0.521884,0.532407,0.307503,0.478305,0.470512,0.629431,0.631734,0.213961,0.41706,0.533176,0.255282,0.696023,0.53587,0.502814,0.0374633,0.236266,0.6812,0.431685,0.404852,0.245626,0.198522,0.611947,0.273479,0.530083,0.44039,0.401506,0.517565,0.582826,0.499348,0.739615|tfbs_overrepresentation_for_novel_motifs=1.51683,0.735382,0.823567,0.440628,0.267236,0.439064,2.20019,0.492582,0.94513,1.21683,0.410439,0.553754,0.40163,0.500805,0.266007,0.782718,0.728104,0.218596,0.842338,0.473089,0.305279,1.347,1.10261,0.262652,0.918075,0.575764,0.729404,1.09816,1.3644,0.329945,1.01144,0.764231,1.06082,0.129565,0.665895,0.261421,0.659326,1.12093,0.611187,0.884996,0.235191,0.374544,0.160114,0.264644,0.301725,0.887061,0.51292,1.0341,0.147122,0.743836,1.4392,0.524278,0.929597,1.9587,0.99088,0.503626,0.273964,0.472204,0.100358,1.18788,0.804523,0.5152,0.162346,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.950736,0.168734,0.53933,0.988898,0.392686,0.741954,0.105027,0.684401,0.750836,0.341765,0.141333,0.699894,0.532172,0.166331,0.937974,1.6482,0.468577,0.659731,1.4924,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.207949,0.136404,0.82268,0.619373,0.606171,0.214313,0.775192,0.817185,0.731699,1.57844,1.04711,0.716172,0.49749,0.347247,1.30109,0.315525,0.814459,0.300169,0.41935,1.12352,0.232218,0.685543,1.00897,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,1.26174,0.785662,1.02292,0.208774,0.911957,1.01734,1.03718,0.539846,1.18405,0.636999,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,1.17257,0.641461,1.83907,0.971016,0.193834,0.86542,1.39433,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.918196,2.35303,2.49645,0.894035,0.750062,0.323817,0.673453,0.531409,0.540317,0.510589,0.100451|tfbs_overrepresentation_jaspar=MA0003.1;0.169975,MA0004.1;0.415381,MA0006.1;0.265592,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.367355,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;2.15039,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;0.264106,MA0050.1;1.04113,MA0051.1;1.27173,MA0052.1;0.795605,MA0055.1;1.02363,MA0056.1;0,MA0057.1;0.539841,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;1.5106,MA0061.1;0.139804,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;1.18425,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;3.19635e-05,MA0074.1;0.509711,MA0076.1;1.61616,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;2.4655,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.271368,MA0103.1;0.714036,MA0105.1;0.496814,MA0106.1;0.554855,MA0107.1;0.205358,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;0.582067,MA0115.1;1.11137,MA0116.1;0.208403,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;1.51455,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.406919,MA0140.1;0.474342,MA0141.1;0.322254,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.1885,MA0145.1;0.39929,MA0146.1;0.319685,MA0147.1;0.211483,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;3.36147,MA0035.2;0.473658,MA0039.2;0.323611,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.780538,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;0.0433683,MA0065.2;0.0483532,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.842081,MA0155.1;1.00468,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.767014,MA0163.1;0.384654,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;0.289676,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.624802,MA0442.1;0}}
|full_id=C867_CD4_CD8_Natural_CD19_Peripheral_cerebellum_Mast
|id=C867
}}

Latest revision as of 11:32, 17 September 2013


Full id: C867_CD4_CD8_Natural_CD19_Peripheral_cerebellum_Mast



Phase1 CAGE Peaks

Hg19::chr10:114206689..114206719,-p2@ZDHHC6
Hg19::chr12:133562945..133562958,+p2@ZNF26
Hg19::chr16:20753114..20753157,-p1@THUMPD1
Hg19::chr19:12273866..12273935,+p1@ZNF136
Hg19::chr19:19843900..19843928,-p1@ZNF14
Hg19::chr1:114354876..114354922,-p1@RSBN1
Hg19::chr3:3221368..3221391,-p1@CRBN
Hg19::chr4:68411182..68411240,-p1@CENPC1
Hg19::chr5:78531917..78531974,+p1@JMY


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
hematopoietic stem cell6.25e-29168
angioblastic mesenchymal cell6.25e-29168
leukocyte7.96e-26136
hematopoietic oligopotent progenitor cell1.89e-25161
hematopoietic multipotent progenitor cell1.89e-25161
hematopoietic cell3.86e-25177
hematopoietic lineage restricted progenitor cell2.80e-19120
nongranular leukocyte1.33e-17115
nucleate cell1.45e-1655
lymphoid lineage restricted progenitor cell3.86e-1652
lymphocyte4.77e-1653
common lymphoid progenitor4.77e-1653
mature alpha-beta T cell1.34e-1118
alpha-beta T cell1.34e-1118
immature T cell1.34e-1118
mature T cell1.34e-1118
immature alpha-beta T cell1.34e-1118
myeloid cell8.09e-11108
common myeloid progenitor8.09e-11108
T cell4.32e-0925
pro-T cell4.32e-0925
CD8-positive, alpha-beta T cell3.09e-0811
myeloid leukocyte1.73e-0772
B cell2.26e-0714
Uber Anatomy
Ontology termp-valuen
adult organism2.65e-33114
neural tube1.55e-1556
neural rod1.55e-1556
future spinal cord1.55e-1556
neural keel1.55e-1556
regional part of nervous system2.05e-1453
regional part of brain2.05e-1453
nervous system6.56e-1489
regional part of forebrain9.65e-1441
forebrain9.65e-1441
anterior neural tube9.65e-1441
future forebrain9.65e-1441
central nervous system2.31e-1381
brain2.67e-1168
future brain2.67e-1168
brain grey matter8.06e-1134
gray matter8.06e-1134
telencephalon1.24e-1034
regional part of telencephalon3.71e-1032
cerebral hemisphere4.32e-1032
regional part of cerebral cortex2.13e-0822
neurectoderm3.03e-0886
hematopoietic system3.24e-0898
blood island3.24e-0898
neural plate9.21e-0882
presumptive neural plate9.21e-0882
cerebral cortex1.21e-0725
pallium1.21e-0725
neocortex1.53e-0720


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)
MA0003.10.169975
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.367355
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.12.15039
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.264106
MA0050.11.04113
MA0051.11.27173
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.10.323879
MA0060.11.5106
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.11.18425
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.11.61616
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.12.4655
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.714036
MA0105.10.496814
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.11.51455
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.406919
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.39929
MA0146.10.319685
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.23.36147
MA0035.20.473658
MA0039.20.323611
MA0138.20.608783
MA0002.20.152495
MA0137.20.780538
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.842081
MA0155.11.00468
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.767014
MA0163.10.384654
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.289676
MA0102.21.41188
MA0258.10.180288
MA0259.10.624802
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#46737.487724842002920.006050357420552810.0268399642630555
BCLAF1#977437.217549203373950.00670404961947760.028500192868833
BRCA1#672511.21346146845763.17534800280252e-050.000637505132765653
CCNT2#90564.224134384641760.000840335063808250.00633719068012635
CHD2#110666.896015222744575.28898897155739e-050.000897443897969914
E2F1#186984.36212374655942.18983367577486e-050.000480874767166213
E2F6#187684.459693983731011.843503537119e-050.000418915722178353
ELF1#199794.258097958807542.17161853202127e-067.81805128803066e-05
ETS1#211366.485840614801567.51193928811803e-050.001163142219884
FOXA2#317038.210154584221750.00467281236756890.0220505987193443
GABPB1#255364.711789224121450.0004576307049007980.00421691311003481
GATA1#262346.026803619466860.002753144894242950.0150992858063246
GTF2F1#296245.662071500781180.00346420020706550.0176005840351096
HEY1#2346294.040111043105713.4850025352467e-060.000115914069993194
HMGN3#932454.543637624083660.002244618319024410.0128897395183697
IRF1#365975.940016252771921.86166156219947e-050.000422765974982714
MXI1#460144.427365168337470.008444657415134930.0327753382057779
MYC#460974.061774789029540.0002355556796573370.00256717099318926
NFKB1#479084.878278599283419.15949022225393e-060.000244469205040117
NFYA#480036.141860233276840.01048163163058090.0388133288138647
NFYB#480135.586597751178820.01358500277111940.0479455293462062
NRF1#489979.496884014886267.65865712776971e-073.36359332114021e-05
PAX5#507975.187439857582764.62776729125731e-050.000812301492658189
POLR2A#543092.147453176558070.001029412892608020.00728294628716227
POU2F2#545266.070749371828350.0001095272295875280.00152336054479849
SETDB1#9869313.44000872600350.001144723251466790.0078365070568917
SIN3A#2594284.807897534946791.02597602607548e-050.000267879775468243
SIX5#14791259.492619641921677.08068365528068e-050.00111757521576826
SP1#666753.16576743230050.01119721686091820.0411176165302709
SRF#672257.665099034537670.0001964447812163450.00236120341874253
TAF1#687293.343046285745291.91655056102793e-050.000433252432993932
TAF7#687945.081364179966180.00514192961203820.0239035870538439
TBP#690893.706770687096397.56501052505806e-060.000215869435581021
TCF7L2#693455.983431423965190.0006305154397321440.00518343844538613
TRIM28#1015548.262455575672230.0008469285971791930.00638322694384049
USF1#739153.534166265115530.00692296754081810.0293079775839279
YY1#752884.365485110981212.17675027117712e-050.000478907987300331
ZNF143#770246.000389578767960.002798128726405460.0153210530595082
ZNF263#1012754.567689798339260.002191305809009130.012632909438458



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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