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Coexpression cluster:C2437: Difference between revisions

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{{Coexpression_clusters
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65,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,1.32255,0.739643,0.821651,0.395818,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,1.31925,0.559384,1.05593,0.471262,0.356737,0.223552,1.42279,0.975621,0.731221,1.3102,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,1.03152,0.53106,0.648765,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,1.37313,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,1.88833,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,1.53017,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.4289|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;1.69588,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;2.32784,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;1.66514,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;1.47358,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;1.52107,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.214613,MA0074.1;0.819248,MA0076.1;1.51122,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;1.02755,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;2.27878,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.656404,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.8309,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;5.55273,MA0035.2;0.778873,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;0.98779,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0626799,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2437_Basophils_CD19_CD14_Eosinophils_CD14CD16_CD34_Neutrophils
|id=C2437
}}

Latest revision as of 12:05, 17 September 2013


Full id: C2437_Basophils_CD19_CD14_Eosinophils_CD14CD16_CD34_Neutrophils



Phase1 CAGE Peaks

Hg19::chr17:7475729..7475754,-p@chr17:7475729..7475754
-
Hg19::chr1:161015811..161015837,+p@chr1:161015811..161015837
+
Hg19::chr1:161015838..161015845,+p@chr1:161015838..161015845
+
Hg19::chr6:109704071..109704117,+p1@BC030091


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
leukocyte1.17e-44136
hematopoietic stem cell4.98e-40168
angioblastic mesenchymal cell4.98e-40168
hematopoietic cell2.05e-39177
hematopoietic lineage restricted progenitor cell1.27e-36120
hematopoietic oligopotent progenitor cell1.63e-36161
hematopoietic multipotent progenitor cell1.63e-36161
nongranular leukocyte2.06e-34115
classical monocyte2.92e-2642
CD14-positive, CD16-negative classical monocyte2.92e-2642
myeloid leukocyte1.03e-2572
granulocyte monocyte progenitor cell3.54e-2267
myeloid cell4.40e-22108
common myeloid progenitor4.40e-22108
myeloid lineage restricted progenitor cell2.80e-2166
defensive cell4.40e-2148
phagocyte4.40e-2148
macrophage dendritic cell progenitor1.16e-2061
monopoietic cell9.50e-2059
monocyte9.50e-2059
monoblast9.50e-2059
promonocyte9.50e-2059
lymphoid lineage restricted progenitor cell5.69e-1452
nucleate cell1.82e-1355
lymphocyte2.97e-1353
common lymphoid progenitor2.97e-1353
stuff accumulating cell9.35e-0987
motile cell1.44e-08386
mature alpha-beta T cell5.20e-0818
alpha-beta T cell5.20e-0818
immature T cell5.20e-0818
mature T cell5.20e-0818
immature alpha-beta T cell5.20e-0818
mesenchymal cell5.40e-08354
lymphocyte of B lineage1.00e-0724
pro-B cell1.00e-0724
connective tissue cell2.20e-07361
intermediate monocyte2.27e-079
CD14-positive, CD16-positive monocyte2.27e-079
B cell4.67e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.57e-2598
blood island9.57e-2598
hemolymphoid system1.60e-21108
bone marrow1.20e-2076
bone element4.02e-1882
immune system1.20e-1793
skeletal element1.81e-1390
skeletal system2.70e-11100
connective tissue7.90e-07371


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)
MA0003.10.443649
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.11.66514
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.25.55273
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#467211.23158726300440.01119559039922220.0411275506754965
BRCA1#672210.09211532161190.0137713969900260.0484723284659384
E2F6#187645.017155731697390.00157802193473060.00996716255466156
ELF1#199744.258097958807540.003041525565781240.0160861846642339
ELK4#2005416.2356816584681.43847748454449e-050.000343233150578803
GABPB1#255347.067683836182170.0004006876864423170.00390258521722924
GATA3#2625213.6182581786030.00769665208093340.0316917933559614
GTF2F1#296239.554745657568240.001820362319304780.0108993189397393
HEY1#2346244.040111043105710.00375304636917980.0185994310406553
IRF1#365947.63716375356390.0002938853996185490.0030745364370191
MYC#460945.22228187160940.001344309395272740.00887529735968704
NANOG#79923214.62238924050630.006698757715363760.028488132463347
REST#597837.237521537096020.004104697304192610.0195784838213633
SETDB1#9869220.16001308900520.00356908685407640.0180850934914796
SIN3A#2594245.408884726815140.001168172384885160.00796102810473219
SIX5#147912417.0867153554591.17257016123224e-050.00029752685876806
SP1#666745.69838137814090.0009482606065333980.00683993297090556
SPI1#668848.204323508522730.000220661881527680.0024946640230428
TAF1#687243.343046285745290.008005664898701650.032211104378607
TAF7#687938.574802053692940.00250055433515240.0140315599725436
TBP#690843.706770687096390.005296377814784350.0244129403565303
TCF7L2#693438.077632422353010.002978381685834620.0158630835273029
THAP1#55145323.52685845213850.0001264251491159520.00168393268059188
TRIM28#10155313.94289378394690.0005972858184258420.00499359058522066
YY1#752844.911170749853860.00171871838055440.0106826893380183



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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