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Coexpression cluster:C2319: Difference between revisions

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{{Coexpression_clusters
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741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,1.62243,1.89595,0.532789,0.559384,1.05593,1.18793,0.356737,0.223552,0.581762,0.169357,1.73475,0.528529,0.632849,0.892087,0.316693,0.728867,1.33003,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,2.13139,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.0946706,4.96586,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.353274,1.84544,0.291738,2.1528,1.89266,1.51507,2.78853,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,2.16273,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,2.59267,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.27972,0.681522,0.988625,0.444962,1.31973,0.932085,1.74599,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,2.73245,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.156682|tfbs_overrepresentation_jaspar=MA0003.1;1.05935,MA0004.1;0.71247,MA0006.1;1.31813,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.34758,MA0017.1;1.41335,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;1.35734,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;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;1.30988,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;0.605914,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;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;2.13662,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,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;1.98562,MA0115.1;1.45393,MA0116.1;2.01976,MA0117.1;2.78257,MA0119.1;1.43218,MA0122.1;2.8366,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;0.912459,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;3.91394,MA0145.1;0.195821,MA0146.1;0.481,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;1.66396,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;1.75253,MA0137.2;3.4512,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;1.09513,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;0.640035,MA0163.1;0.539587,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;1.88931,MA0259.1;1.1888,MA0442.1;0}}
|full_id=C2319_Eosinophils_large_immature_Neutrophils_small_migratory_Mast
|id=C2319
}}

Latest revision as of 12:03, 17 September 2013


Full id: C2319_Eosinophils_large_immature_Neutrophils_small_migratory_Mast



Phase1 CAGE Peaks

Hg19::chr14:88459407..88459418,-p4@GALC
Hg19::chr14:88459424..88459442,-p5@GALC
Hg19::chr14:88459457..88459484,-p2@GALC
Hg19::chr14:88459487..88459500,-p3@GALC


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 leukocyte8.67e-3072
myeloid cell1.27e-28108
common myeloid progenitor1.27e-28108
granulocyte monocyte progenitor cell6.93e-2767
myeloid lineage restricted progenitor cell2.13e-2566
macrophage dendritic cell progenitor4.19e-2361
leukocyte4.83e-22136
defensive cell4.83e-2248
phagocyte4.83e-2248
monopoietic cell7.17e-2259
monocyte7.17e-2259
monoblast7.17e-2259
promonocyte7.17e-2259
hematopoietic oligopotent progenitor cell8.82e-22161
hematopoietic multipotent progenitor cell8.82e-22161
hematopoietic stem cell1.75e-21168
angioblastic mesenchymal cell1.75e-21168
classical monocyte4.95e-2042
CD14-positive, CD16-negative classical monocyte4.95e-2042
hematopoietic cell1.57e-19177
hematopoietic lineage restricted progenitor cell2.09e-17120
nongranular leukocyte1.55e-14115
stuff accumulating cell5.74e-0887
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.47e-2798
blood island4.47e-2798
adult organism1.54e-26114
hemolymphoid system4.53e-24108
bone marrow3.27e-2176
bone element1.27e-1982
immune system2.31e-1993
skeletal element4.09e-1790
skeletal system1.09e-15100
neural tube8.26e-1456
neural rod8.26e-1456
future spinal cord8.26e-1456
neural keel8.26e-1456
lateral plate mesoderm2.24e-12203
regional part of nervous system2.31e-1253
regional part of brain2.31e-1253
regional part of forebrain1.94e-1141
forebrain1.94e-1141
anterior neural tube1.94e-1141
future forebrain1.94e-1141
brain grey matter2.03e-0934
gray matter2.03e-0934
telencephalon4.08e-0934
central nervous system6.29e-0981
regional part of telencephalon1.50e-0832
cerebral hemisphere3.15e-0832
musculoskeletal system8.74e-08167
brain1.31e-0768
future brain1.31e-0768
neural plate1.39e-0782
presumptive neural plate1.39e-0782
regional part of cerebral cortex2.67e-0722
nervous system3.95e-0789


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)
MA0003.11.05935
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.12.13662
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.12.01976
MA0117.12.78257
MA0119.11.43218
MA0122.12.8366
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.13.91394
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.21.75253
MA0137.23.4512
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.21.09513
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
MA0162.10.640035
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.11.88931
MA0259.11.1888
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#467422.46317452600873.92475754624726e-060.000127218421282594
BCL11A#53335428.36945510360711.542446414682e-065.8856982500173e-05
CTCF#1066445.360256373075030.001211145381643620.00816280411160805
E2F1#186944.907389214879320.001724022357361790.010637157853164
E2F6#187645.017155731697390.00157802193473060.00995993429874473
ELF1#199744.258097958807540.003041525565781240.016072348136239
GATA1#2623413.56030814380042.95627390049268e-050.000613573708055554
HEY1#2346244.040111043105710.00375304636917980.018576512310463
IRF1#365947.63716375356390.0002938853996185490.00307115241652608
IRF4#3662421.91451268674414.33289161192893e-060.000136220008145167
MAX#414946.452555509007120.0005767613195645490.00484955925078511
NFKB1#479045.488063424193840.001102199566301980.00767315161345236
PAX5#507946.669565531177830.0005052774169483260.00443450992845934
POU2F2#545249.106124057742520.000145395665174930.00188235749041831
SIN3A#2594245.408884726815140.001168172384885160.00795272509647486
SIX5#147912417.0867153554591.17257016123224e-050.000297310160400421
TAF1#687243.343046285745290.008005664898701650.0321702053234129
TBP#690843.706770687096390.005296377814784350.0243806594939291
TCF12#6938410.63446490218647.8163066689251e-050.00119924673453191
THAP1#55145431.36914460285131.03171810326891e-064.31351509156532e-05
USF1#739146.361499277207960.0006105011399140830.00507401946136296
USF2#7392412.99219738506963.50833029870167e-050.000680673431295009
YY1#752844.911170749853860.00171871838055440.0106699892377531
ZNF263#1012748.221841637010680.0002187871180958320.00248395562852599



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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