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Coexpression cluster:C1306: Difference between revisions

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{{Coexpression_clusters
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2559,0.164471,0.533328,0.313891,0.292462,0.46896,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.441686,0.369492,0.592234|tfbs_overrepresentation_for_novel_motifs=1.97464,0.946942,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.555913,1.36279,0.707204,0.223349,0.650887,0.391663,1.06849,2.06078,0.336106,0.236034,0.127969,0.436569,0.6169,1.41165,0.387783,0.483957,0.730467,0.202389,0.574247,1.02557,0.186644,0.530785,0.92701,0.816912,0.225641,0.35719,2.82399,0.35388,1.43099,0.329602,1.9886,0.355745,0.513952,0.0979105,0.390088,0.354447,0.468392,0.66382,1.33909,0.0909286,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,0.861462,1.63815,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,2.00082,0.684313,0.272514,1.10535,1.10459,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.962826,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,2.62193,0.44815,0.978783,0.430775,0.563054,2.88157,0.928633,0.800507,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,1.58608,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,1.49651,0.424432,0.308967,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,2.00817,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,2.36361|tfbs_overrepresentation_jaspar=MA0003.1;1.37104,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;6.41866,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;2.63632,MA0027.1;2.65688,MA0028.1;1.05129,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.465994,MA0056.1;0,MA0057.1;2.74001,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.671725,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.720548,MA0074.1;0.660398,MA0076.1;1.19721,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;2.61648,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;1.25994,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;1.19942,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;3.48752,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;0.621793,MA0039.2;3.75773,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;2.25875,MA0065.2;1.18263,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.819655,MA0155.1;0.318517,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;1.57484,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.87239,MA0163.1;0.508943,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;14.2201,MA0102.2;1.58513,MA0258.1;1.43672,MA0259.1;0.336472,MA0442.1;0}}
|full_id=C1306_CD4_Mast_Basophils_Natural_CD19_CD14_CD8
|id=C1306
}}

Latest revision as of 11:42, 17 September 2013


Full id: C1306_CD4_Mast_Basophils_Natural_CD19_CD14_CD8



Phase1 CAGE Peaks

Hg19::chr10:22725987..22726012,+p1@LOC100289455
Hg19::chr15:66084798..66084817,+p@chr15:66084798..66084817
+
Hg19::chr1:245134140..245134165,+p@chr1:245134140..245134165
+
Hg19::chr22:41809910..41809952,-p@chr22:41809910..41809952
-
Hg19::chr9:3526047..3526146,+p1@AK125504
Hg19::chr9:3526461..3526499,+p1@ENST00000423112


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
leukocyte1.61e-41136
hematopoietic stem cell1.10e-39168
angioblastic mesenchymal cell1.10e-39168
hematopoietic cell2.16e-37177
hematopoietic lineage restricted progenitor cell6.21e-37120
hematopoietic oligopotent progenitor cell5.94e-36161
hematopoietic multipotent progenitor cell5.94e-36161
nongranular leukocyte4.35e-35115
classical monocyte2.11e-2142
CD14-positive, CD16-negative classical monocyte2.11e-2142
myeloid leukocyte1.33e-2072
granulocyte monocyte progenitor cell2.38e-1967
myeloid lineage restricted progenitor cell5.41e-1966
defensive cell9.24e-1948
phagocyte9.24e-1948
myeloid cell1.19e-18108
common myeloid progenitor1.19e-18108
nucleate cell1.90e-1755
macrophage dendritic cell progenitor2.56e-1761
lymphocyte1.05e-1653
common lymphoid progenitor1.05e-1653
lymphoid lineage restricted progenitor cell1.26e-1652
monopoietic cell1.35e-1659
monocyte1.35e-1659
monoblast1.35e-1659
promonocyte1.35e-1659
mature alpha-beta T cell5.27e-1118
alpha-beta T cell5.27e-1118
immature T cell5.27e-1118
mature T cell5.27e-1118
immature alpha-beta T cell5.27e-1118
T cell1.36e-0825
pro-T cell1.36e-0825
B cell7.16e-0814
CD8-positive, alpha-beta T cell1.13e-0711
lymphocyte of B lineage1.23e-0724
pro-B cell1.23e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.70e-2398
blood island3.70e-2398
hemolymphoid system4.91e-21108
bone marrow1.42e-1776
immune system5.61e-1793
bone element7.75e-1582
adult organism2.90e-13114
neural tube6.41e-1256
neural rod6.41e-1256
future spinal cord6.41e-1256
neural keel6.41e-1256
regional part of nervous system2.21e-1153
regional part of brain2.21e-1153
skeletal element1.59e-1090
skeletal system5.02e-09100
central nervous system6.09e-0981
regional part of forebrain8.88e-0941
forebrain8.88e-0941
anterior neural tube8.88e-0941
future forebrain8.88e-0941
nervous system1.63e-0889
brain1.12e-0768
future brain1.12e-0768
telencephalon3.28e-0734
neurectoderm3.58e-0786
brain grey matter3.94e-0734
gray matter3.94e-0734


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)
MA0003.11.37104
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.16.41866
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.12.63632
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.12.74001
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.720548
MA0074.10.660398
MA0076.11.19721
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.12.61648
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.13.48752
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.23.75773
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.22.25875
MA0065.21.18263
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.11.57484
MA0160.10.600559
MA0161.10
MA0162.11.87239
MA0163.10.508943
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.214.2201
MA0102.21.58513
MA0258.11.43672
MA0259.10.336472
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#90544.224134384641760.007109805478875810.0296057164550182
CTCF#1066443.573504248716680.01316635007238510.0465986795625006
E2F1#186954.089491012399440.001749817597761990.0107550141297472
E2F4#187436.334030157642220.008197175368374340.0323571244348646
E2F6#187654.180963109747820.001573598759586970.00997239568279753
GABPB1#255344.711789224121450.004730054311555960.0222834653004012
GTF2F1#296236.369830438378830.008068208196303160.031909554126319
HEY1#2346253.366759202588090.004423827045203030.020946641554788
MYC#460954.35190155967450.001297956345724110.008696257556523
NFKB1#479043.658708949462560.01207927289015230.0438189364840089
PAX5#507955.557971275981520.0003977176196612860.00388488874670829
POLR2A#543062.147453176558070.01019570676818780.0379807896690957
POU2F2#545257.588436714785448.70203885493171e-050.0012900386600003
SIN3A#2594254.507403939012610.001096110061208640.00765730024632567
SMARCB1#659839.126357890578710.002900247150367020.0156739411196471
TAF1#687263.343046285745290.0007162474284635620.00572378645506971
TAF7#687935.716534702461960.01092729379889660.0402070052516545
TBP#690863.706770687096390.000385416472907960.00377426263610262
TCF7L2#693435.385088281568670.01290488779931040.0463965567445411
TFAP2C#702235.404614304930110.01277576166695870.0460575689587678
YY1#752864.911170749853867.12445972864136e-050.00112312671637672
ZNF263#1012745.481227758007120.002675609380607230.0147406218336888



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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