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Coexpression cluster:C817: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.280498,0.216121,0.273994,0.404877,1.24375,0.403356,0.474413,0.434224,0.847231,0.0921938,0.375531,0.515448,0.107365,0.46359,0.236531,0.712999,0.68716,0.191625,0.748636,0.0470551,0.274046,0.805814,0.396189,0.233338,0.314616,0.537051,0.641011,0.39419,0.240354,0.590419,0.355553,0.722879,0.495657,0.108961,0.20845,1.1313,0.20579,1.04333,0.547451,1.28559,1.76615,0.340749,1.7121,0.235234,0.111933,0.301189,0.47544,0.365597,0.279701,0.675323,0.550604,0.486559,0.0591862,0.797754,0.947672,0.466348,0.244111,1.11117,0.281305,0.434711,0.762758,1.20168,0.139078,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.144996,0.462053,0.945703,0.339984,0.0955465,0.292851,0.644006,0.709631,0.309107,0.380738,0.659298,0.49429,0.439665,0.89511,0.0102458,0.0463436,0.575051,0.575506,1.4989,1.12715,0.868602,0.739223,0.509773,1.93329,0.18161,0.368981,0.780743,0.579925,0.524614,1.65658,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.844195,0.22412,1.41517,0.772599,0.269151,0.384185,1.07963,0.204477,0.171258,0.354459,0.624851,0.991665,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.537508,0.869279,0.358161,0.993705,0.50181,1.13991,0.0752959,0.350108,1.02211,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,4.88623,1.79367,0.337738,0.168379,0.052013,0.285345,0.869654,0.414185,0.477214,1.26919,0.560015,0.64107,0.314669,0.28899,1.05976,0.851493,1.68841,0.291837,0.633206,0.493542,0.158769,0.473159,0.02648
|tfbs_overrepresentation_jaspar=MA0003.1;0.0250581,MA0004.1;0.380329,MA0006.1;0.236135,MA0007.1;1.69684,MA0009.1;0.828613,MA0014.1;0.15363,MA0017.1;0.270554,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;2.20595,MA0027.1;2.43535,MA0028.1;0.25013,MA0029.1;2.9484,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;0.477043,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;0.817858,MA0048.1;0.220931,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.174262,MA0056.1;0,MA0057.1;0.211138,MA0058.1;0.293055,MA0059.1;0.291897,MA0060.1;0.138988,MA0061.1;3.1466,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.631708,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;0.00880943,MA0074.1;0.4723,MA0076.1;0.307383,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.79376,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;0.55119,MA0089.1;0,MA0090.1;1.54714,MA0091.1;0.382762,MA0092.1;0.347826,MA0093.1;0.238771,MA0095.1;0,MA0098.1;0,MA0100.1;0.49029,MA0101.1;6.5191,MA0103.1;0.646502,MA0105.1;2.12449,MA0106.1;0.516528,MA0107.1;5.66423,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.885497,MA0113.1;0.532314,MA0114.1;0.174997,MA0115.1;1.06753,MA0116.1;0.182037,MA0117.1;0.865782,MA0119.1;3.88311,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;0.353333,MA0140.1;0.437738,MA0141.1;0.290336,MA0142.1;1.54256,MA0143.1;0.532484,MA0144.1;1.51733,MA0145.1;0.0359093,MA0146.1;0.128432,MA0147.1;0.184931,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.114378,MA0035.2;0.437071,MA0039.2;0.0109452,MA0138.2;0.569505,MA0002.2;0.129981,MA0137.2;2.02481,MA0104.2;0.138396,MA0047.2;0.504873,MA0112.2;0.133417,MA0065.2;0.615279,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;1.12157,MA0155.1;0.030416,MA0156.1;0.257809,MA0157.1;1.4867,MA0158.1;0,MA0159.1;0.185458,MA0160.1;0.417847,MA0161.1;0,MA0162.1;0.108522,MA0163.1;0.0728181,MA0164.1;0.544294,MA0080.2;0.671553,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;0.0179307,MA0102.2;1.36707,MA0258.1;0.472117,MA0259.1;0.560522,MA0442.1;0
}}
}}

Revision as of 19:28, 22 January 2013


Full id: C817_cord_CD14_mycosis_xeroderma_migratory_B_hairy



Phase1 CAGE Peaks

Hg19::chr12:24858680..24858711,-p@chr12:24858680..24858711
-
Hg19::chr12:39300630..39300641,-p@chr12:39300630..39300641
-
Hg19::chr12:47787958..47787968,-p@chr12:47787958..47787968
-
Hg19::chr17:40440359..40440386,+p4@STAT5A
Hg19::chr2:223288634..223288698,+p2@SGPP2
Hg19::chr3:47032286..47032317,+p@chr3:47032286..47032317
+
Hg19::chr6:138192164..138192180,+p4@TNFAIP3
Hg19::chr6:138192205..138192214,+p15@TNFAIP3
Hg19::chr6:138192259..138192268,+p18@TNFAIP3
Hg19::chr8:145086442..145086455,+p2@SPATC1


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:0006916anti-apoptosis0.0098087440622032
GO:0046544development of secondary male sexual characteristics0.0098087440622032
GO:0001779natural killer cell differentiation0.0098087440622032
GO:0001553luteinization0.0098087440622032
GO:0046543development of secondary female sexual characteristics0.0098087440622032
GO:0043066negative regulation of apoptosis0.0098087440622032
GO:0043069negative regulation of programmed cell death0.0098087440622032
GO:0045136development of secondary sexual characteristics0.010829102476073
GO:0045647negative regulation of erythrocyte differentiation0.010829102476073
GO:0045579positive regulation of B cell differentiation0.010829102476073
GO:0045931positive regulation of progression through mitotic cell cycle0.010829102476073
GO:0043029T cell homeostasis0.010829102476073
GO:0042104positive regulation of activated T cell proliferation0.010829102476073
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.010829102476073
GO:0007243protein kinase cascade0.010829102476073
GO:0045621positive regulation of lymphocyte differentiation0.010829102476073
GO:0046006regulation of activated T cell proliferation0.010829102476073
GO:0030856regulation of epithelial cell differentiation0.010829102476073
GO:0050798activated T cell proliferation0.010829102476073
GO:0019915sequestering of lipid0.010829102476073
GO:0045885positive regulation of survival gene product activity0.010829102476073
GO:0045577regulation of B cell differentiation0.010829102476073
GO:0019218regulation of steroid metabolic process0.0116977484600152
GO:0002260lymphocyte homeostasis0.0116977484600152
GO:0050729positive regulation of inflammatory response0.0116977484600152
GO:0045086positive regulation of interleukin-2 biosynthetic process0.0116977484600152
GO:0031349positive regulation of defense response0.0116977484600152
GO:0045646regulation of erythrocyte differentiation0.0116977484600152
GO:0040018positive regulation of multicellular organism growth0.0123205953733832
GO:0030879mammary gland development0.0125345319247793
GO:0001776leukocyte homeostasis0.0125345319247793
GO:0042981regulation of apoptosis0.0125345319247793
GO:0043067regulation of programmed cell death0.0125345319247793
GO:0048872homeostasis of number of cells0.0125345319247793
GO:0045076regulation of interleukin-2 biosynthetic process0.0125345319247793
GO:0045884regulation of survival gene product activity0.0125345319247793
GO:0042094interleukin-2 biosynthetic process0.0125345319247793
GO:0045619regulation of lymphocyte differentiation0.0125345319247793
GO:0030101natural killer cell activation0.0130683881921848
GO:0050871positive regulation of B cell activation0.0130683881921848
GO:0045638negative regulation of myeloid cell differentiation0.0130683881921848
GO:0005737cytoplasm0.0137767055420435
GO:0032623interleukin-2 production0.0137767055420435
GO:0007595lactation0.0137767055420435
GO:0040014regulation of multicellular organism growth0.0137767055420435
GO:0045927positive regulation of growth0.0137767055420435
GO:0035264multicellular organism growth0.0137767055420435
GO:0045787positive regulation of progression through cell cycle0.0137767055420435
GO:0022601menstrual cycle phase0.0137767055420435
GO:0031347regulation of defense response0.0137767055420435
GO:0050727regulation of inflammatory response0.0137767055420435
GO:0042102positive regulation of T cell proliferation0.0137767055420435
GO:0022602menstrual cycle process0.0137767055420435
GO:0050864regulation of B cell activation0.0137767055420435
GO:0008585female gonad development0.0145156931210802
GO:0019216regulation of lipid metabolic process0.0145156931210802
GO:0030183B cell differentiation0.0145156931210802
GO:0046545development of primary female sexual characteristics0.0145156931210802
GO:0046660female sex differentiation0.0145156931210802
GO:0032946positive regulation of mononuclear cell proliferation0.0145156931210802
GO:0050671positive regulation of lymphocyte proliferation0.0145156931210802
GO:0006915apoptosis0.0145156931210802
GO:0012501programmed cell death0.0145156931210802
GO:0046661male sex differentiation0.0145156931210802
GO:0007346regulation of progression through mitotic cell cycle0.0145156931210802
GO:0030218erythrocyte differentiation0.0145156931210802
GO:0042698menstrual cycle0.0145156931210802
GO:0042129regulation of T cell proliferation0.0145156931210802
GO:0045637regulation of myeloid cell differentiation0.0145156931210802
GO:0048583regulation of response to stimulus0.0145156931210802
GO:0008219cell death0.0145156931210802
GO:0016265death0.0145156931210802
GO:0030855epithelial cell differentiation0.0146678950118608
GO:0042098T cell proliferation0.0154644313545556
GO:0007259JAK-STAT cascade0.0154644313545556
GO:0042108positive regulation of cytokine biosynthetic process0.0158086676443632
GO:0050870positive regulation of T cell activation0.0158086676443632
GO:0050670regulation of lymphocyte proliferation0.0158086676443632
GO:0032944regulation of mononuclear cell proliferation0.0158086676443632
GO:0019221cytokine and chemokine mediated signaling pathway0.0159820453218798
GO:0048732gland development0.0168837595886084
GO:0051251positive regulation of lymphocyte activation0.0181058406720078
GO:0008406gonad development0.0181058406720078
GO:0048608reproductive structure development0.0181058406720078
GO:0032943mononuclear cell proliferation0.0181058406720078
GO:0045727positive regulation of translation0.0181058406720078
GO:0046651lymphocyte proliferation0.0181058406720078
GO:0048523negative regulation of cellular process0.0184569630324013
GO:0048519negative regulation of biological process0.0188784886440321
GO:0050863regulation of T cell activation0.0188784886440321
GO:0045137development of primary sexual characteristics0.0188784886440321
GO:0042035regulation of cytokine biosynthetic process0.0188784886440321
GO:0031328positive regulation of cellular biosynthetic process0.0188784886440321
GO:0048609reproductive process in a multicellular organism0.0188784886440321
GO:0032504multicellular organism reproduction0.0188784886440321
GO:0042113B cell activation0.0188784886440321
GO:0002009morphogenesis of an epithelium0.0192947462408728
GO:0030098lymphocyte differentiation0.0193083537645488
GO:0048468cell development0.0193083537645488
GO:0045596negative regulation of cell differentiation0.0193083537645488
GO:0030155regulation of cell adhesion0.019410435056621
GO:0042089cytokine biosynthetic process0.0195104890621031
GO:0042107cytokine metabolic process0.0196085748296782
GO:0009891positive regulation of biosynthetic process0.019989442238841
GO:0051249regulation of lymphocyte activation0.0213652824192219
GO:0030099myeloid cell differentiation0.0213652824192219
GO:0051093negative regulation of developmental process0.0213652824192219
GO:0050865regulation of cell activation0.0218583455770107
GO:0007565female pregnancy0.0218583455770107
GO:0007548sex differentiation0.0218583455770107
GO:0051247positive regulation of protein metabolic process0.0225908458224773
GO:0043229intracellular organelle0.0225908458224773
GO:0043226organelle0.0225908458224773
GO:0003006reproductive developmental process0.022647707531505
GO:0002521leukocyte differentiation0.0232218577750432
GO:0042110T cell activation0.0250591822261653
GO:0009968negative regulation of signal transduction0.0263591358542017
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0271361788289405
GO:0001816cytokine production0.028147672630088
GO:0005813centrosome0.0318428891726392
GO:0048869cellular developmental process0.0328468075171884
GO:0030154cell differentiation0.0328468075171884
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0331898449785698
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0331898449785698
GO:0045595regulation of cell differentiation0.0341011196355686
GO:0005815microtubule organizing center0.0345306996525982
GO:0046649lymphocyte activation0.0361104615281305
GO:0007242intracellular signaling cascade0.0366690693465053
GO:0030097hemopoiesis0.0369169725815447
GO:0048534hemopoietic or lymphoid organ development0.0393425365237529
GO:0045321leukocyte activation0.0404395778703146
GO:0044424intracellular part0.0404395778703146
GO:0002520immune system development0.0404395778703146
GO:0006417regulation of translation0.0405752779607144
GO:0031326regulation of cellular biosynthetic process0.0435291181174172
GO:0040008regulation of growth0.0436394550898104
GO:0001775cell activation0.0450292094685027
GO:0009889regulation of biosynthetic process0.0463976173369759
GO:0045893positive regulation of transcription, DNA-dependent0.0469868872906378
GO:0008202steroid metabolic process0.0469868872906378
GO:0008284positive regulation of cell proliferation0.0487241955275788
GO:0050793regulation of developmental process0.0489975011728461



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
leukocyte1.31e-48136
myeloid leukocyte3.81e-4672
granulocyte monocyte progenitor cell5.63e-4167
defensive cell1.20e-4048
phagocyte1.20e-4048
myeloid lineage restricted progenitor cell1.63e-3966
macrophage dendritic cell progenitor2.53e-3961
classical monocyte2.88e-3942
CD14-positive, CD16-negative classical monocyte2.88e-3942
hematopoietic cell9.55e-39177
monopoietic cell1.10e-3859
monocyte1.10e-3859
monoblast1.10e-3859
promonocyte1.10e-3859
hematopoietic lineage restricted progenitor cell2.07e-38120
nongranular leukocyte1.41e-37115
hematopoietic stem cell6.02e-37168
angioblastic mesenchymal cell6.02e-37168
hematopoietic oligopotent progenitor cell2.26e-36161
hematopoietic multipotent progenitor cell2.26e-36161
myeloid cell6.20e-34108
common myeloid progenitor6.20e-34108
stuff accumulating cell1.47e-2187
conventional dendritic cell8.39e-138
mesenchymal cell2.66e-11354
connective tissue cell9.94e-11361
dendritic cell3.52e-1010
circulating cell3.73e-096
motile cell9.69e-09386
immature conventional dendritic cell1.16e-075
common dendritic progenitor1.16e-075
multi fate stem cell3.03e-07427
stem cell6.09e-07441
somatic stem cell6.61e-07433
Langerhans cell6.75e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.44e-4198
blood island3.44e-4198
hemolymphoid system2.02e-39108
immune system1.00e-3793
bone marrow1.27e-3476
bone element3.63e-3182
skeletal element2.78e-2790
skeletal system2.59e-23100
lateral plate mesoderm3.93e-15203
musculoskeletal system5.25e-10167
connective tissue5.94e-10371
mesoderm8.42e-09315
mesoderm-derived structure8.42e-09315
presumptive mesoderm8.42e-09315


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)
MA0003.10.0250581
MA0004.10.380329
MA0006.10.236135
MA0007.11.69684
MA0009.10.828613
MA0014.10.15363
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.12.20595
MA0027.12.43535
MA0028.10.25013
MA0029.12.9484
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.174262
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.13.1466
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.631708
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.00880943
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.79376
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.55119
MA0089.10
MA0090.11.54714
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.16.5191
MA0103.10.646502
MA0105.12.12449
MA0106.10.516528
MA0107.15.66423
MA0108.20.666881
MA0109.10
MA0111.10.885497
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.13.88311
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.353333
MA0140.10.437738
MA0141.10.290336
MA0142.11.54256
MA0143.10.532484
MA0144.11.51733
MA0145.10.0359093
MA0146.10.128432
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.0109452
MA0138.20.569505
MA0002.20.129981
MA0137.22.02481
MA0104.20.138396
MA0047.20.504873
MA0112.20.133417
MA0065.20.615279
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.11.12157
MA0155.10.030416
MA0156.10.257809
MA0157.11.4867
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.10.0728181
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.20.0179307
MA0102.21.36707
MA0258.10.472117
MA0259.10.560522
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
EBF1#187965.34388010794140.0002809265931316460.00298988000204585
IRF4#3662510.95725634337214.10495409675721e-050.000745854733666017
NFKB1#479094.939257081774451.84959706943667e-066.85973254030173e-05
TCF12#693844.253785960874570.01031118060518840.0383002948829986



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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