Coexpression cluster:C28: Difference between revisions
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|id=C28 | |id=C28 | ||
|kegg_enrichment=hsa04640;Hematopoietic_cell_lineage;0.000109558 | |kegg_enrichment=hsa04640;Hematopoietic_cell_lineage;0.000109558 | ||
|ontology_enrichment_celltype= | |ontology_enrichment_celltype= | ||
|ontology_enrichment_disease= | |ontology_enrichment_disease= | ||
|ontology_enrichment_uberon=UBERON: | |ontology_enrichment_uberon=UBERON:0004177!6.03e-43!7;UBERON:0005057!6.03e-43!7;UBERON:0002370!4.28e-34!4;UBERON:0005058!4.28e-34!4;UBERON:0009113!4.28e-34!4;UBERON:0003295!4.28e-34!4;UBERON:0005562!4.28e-34!4;UBERON:0000974!1.86e-30!10;UBERON:0003351!3.88e-23!6;UBERON:0000341!9.07e-18!2;UBERON:0003408!2.49e-14!10;UBERON:0001042!2.49e-14!10;UBERON:0009145!2.49e-14!10;UBERON:0006562!4.00e-13!11;UBERON:0009722!4.00e-13!11;UBERON:0007690!4.00e-13!11;UBERON:0002106!3.24e-12!3;UBERON:0004854!3.24e-12!3;UBERON:0009034!3.24e-12!3;UBERON:0002095!3.24e-12!3;UBERON:0004782!3.24e-12!3;UBERON:0003281!3.24e-12!3;UBERON:0009664!3.24e-12!3;UBERON:0002296!3.24e-12!3;UBERON:0005602!3.24e-12!3;UBERON:0001179!3.24e-12!3;UBERON:0006293!3.24e-12!3;UBERON:0000077!4.97e-11!29;UBERON:0008814!2.09e-08!18;UBERON:0001557!5.16e-08!19 | ||
|pathway_enrichment=6.54052691149315e-09;4.14015353497516e-06;7;88;Hematopoietic cell lineage (KEGG):04640!3.09376651138622e-06;0.000652784733902493;4;35;Primary immunodeficiency (KEGG):05340!4.16631468269243e-05;0.00659319298536076;5;133;T Cell Receptor Signaling Pathway (Wikipathways):WP69!0.000209864686631542;0.0265688693275532;6;295;IL-2 down reg. targets (Netpath):NetPath_14!3.66016971681764e-07;0.000115844371537278;5;51;{HLA-A,53} (Static Module):NA | |pathway_enrichment=6.54052691149315e-09;4.14015353497516e-06;7;88;Hematopoietic cell lineage (KEGG):04640!3.09376651138622e-06;0.000652784733902493;4;35;Primary immunodeficiency (KEGG):05340!4.16631468269243e-05;0.00659319298536076;5;133;T Cell Receptor Signaling Pathway (Wikipathways):WP69!0.000209864686631542;0.0265688693275532;6;295;IL-2 down reg. targets (Netpath):NetPath_14!3.66016971681764e-07;0.000115844371537278;5;51;{HLA-A,53} (Static Module):NA | ||
|tfbs_overrepresentation=0.9986,0.9355,1,0.88397,0.999902,0.999999,0.981609,1,0.916336,0.99571,0.999591,1,0.992716,0.900073,0.995676,0.99922,0.994301,0.199809,0.996276,0.998873,0.995509,0.913326,0.852493,0.9988,0.941156,0.999953,0.999975,1,0.978504,0.999825,1,0.989513,0.97783,0.999752,0.998668,0.391636,1,0.981497,0.999531,0.998708,0.849086,0.764057,0.999999,0.988343,0.998972,0.999559,0.960753,0.985189,0.999292,0.900019,0.987321,0.894574,0.455321,0.998411,0.931086,0.988242,0.978243,1,0.868634,0.928054,0.998076,0.999493,0.532484,0.992764,0.50914,0.846522,0.999996,0.973416,0.980113,0.964419,0.999999,0.792364,0.951688,0.999925,0.209141,0.875713,0.997609,0.995308,0.996834,0.450084,0.987367,0.999921,0.994208,0.995105,0.999998,1,0.998087,1,1,0.9926,0.60142,0.999976,0.999992,0.999961,0.999351,0.990634,1,0.999876,0.999998,0.999919,0.963269,0.989261,0.990776,0.95487,0.994319,0.97466,0.998768,0.976026,0.999915,1,1,0.975299,0.999776,0.976134,0.999954,0.927501,0.928171,0.99805,0.999568,0.997659,0.999065,0.999297,0.99963,0.995558,0.999871,0.931005,0.994707,0.0964838,0.955205,0.999949,0.988232,0.999926,0.993987,0.991974,0.999481,0.994446,0.645337,0.997556,0.999118,0.56378,0.859617,0.999072,0.989734,0.999796,1,0.963282,0.99598,0.999763,0.965794,0.2421,0.986041,0.999492,0.963963,0.996446,0.994417,0.998372,0.980992,0.962943,0.925872,0.993778,0.999964,0.999595,0.999883,0.920648,0.740931,0.999545,0.927924,0.999586,0.930891,0.777014,0.995889,0.997685,0.665925,0.944459,0.979238,0.97594,0.999999,0.998156,0.938469,0.995679,0.999697,0.699192,0.997024,0.983806,0.999909,0.997041,0.999991,0.971588,0.971221,0.997333,0.987721,0.986651,0.999679,0.999592,0.998603,0.990348,0.633718,0.538681,0.996477,0.999879,0.921674,0.751841,0.989256,0.975402,0.983707,1,0.998806,0.885418,0.981113,0.956333,0.988286,0.983155,0.956124,0.999978,0.999031,0.999999,1,0.999952,0.797794,0.994925,0.994885,0.998998,0.557059,0.999026,0.996154,0.999539,0.999999,0.990193,0.902663,0.973023,1,1,0.943225,0.968896,0.451742,1,0.877683,0.999943,0.999656,1,0.999884,1,0.99097,0.914036,0.999959,1,0.998801,0.998392,0.999983,0.751568,0.997618,0.999994,0.984555,0.995535,0.741975,0.997788,0.998735,0.981174,0.982985,1,0.979329,1,1,0.992686,0.994646,0.996492,0.982113,0.980809,0.99997,1,1,0.982793,1,1,0.999842,0.987475,0.98946,0.999259,1,0.995917,0.999118,0.999812,1,1,0.987503,1,0.97378,0.844113,0.28342,0.999922,0.937752,0.994846,1,0.999952,0.999599,0.995246,0.984468,0.999865,0.999462,1,1,0.98647,0.969507,0.608881,0.999467,0.986063,0.99967,0.999977,0.990532,1,0.878084,0.968066,1,0.998467,0.999995,0.996506,0.99997,1,0.676846,0.996811,0.999802,0.999098,0.999066,0.998669,0.893166,1,0.869732,1,0.999821,0.999986,0.948721,1,1,0.174013,0.999954,0.966132,1,0.999869,0.999044,0.99906,1,1,1,0.98366,0.999995,0.83907,0.999995,0.985613,0.999963,1,0.99817,1,1,0.980098,0.750999,0.999984,0.995194,0.291424,0.976644,0.989187,1,1,0.997661,1,0.684429,0.652556,0.999999,1,0.979593,1,1,0.747793,0.999925,0.826076,1,1,1,0.959749,0.984164,1,1,1,1,0.157311,1,0.999924,0.999984,0.996995,0.992292,0.999987,1,0.999813,0.993794,0.989012,0.999713,1,0.937362,0.969094,0.955552,0.999773,1,1,0.99999,0.91064,0.999941,0.868796,0.99518,0.999993,0.999225,0.505072,0.941453,0.981926,0.744929,0.999053,0.936603,0.98752,0.99414,0.52396,1,0.951838,0.999996,0.994738,0.989672,0.998437,0.999684,0.999988,1,1,0.999917,0.999956,0.993707,1,0.548798,0.105309,1,0.939966,0.999706,0.944456,1,0.999422,0.806031,1,0.999925,0.999958,0.920489,0.824397,0.600525,1,0.896285,0.999987,0.754993,0.999876,0.999997,0.875689,1,0.914538,0.965176,0.757041,1,0.994565,0.926996,0.997978,0.991065,0.997498,1,1,1,0.999993,1,0.820707,1,0.934573,0.999232,0.342141,1,0.99265,1,0.891184,0.999747,1,1,0.663089,1,0.78095,0.999252,0.829162,0.999474,0.95589,0.937227,0.999916,0.196976,0.978871,0.988226,1,1,1,0.743361,0.278471,0.998706,0.756901,0.9745,0.999602,0.999911,1,0.999991,1,0.9979,0.999955,1,0.999844,0.999974,0.999276,0.998684,0.999868,0.834443,0.906478,0.999999,0.993666,0.99998,0.635782,0.999998,0.99849,0.722355,0.998324,0.999462,0.960596,0.931403,0.999999,0.995306,0.999499,0.997901,0.999981,0.999988,0.999724,0.954701,1,1,0.999988,0.812313,0.999604,0.998271,1,0.995997,0.997117,0.999567,0.999884,0.999392,0.999959,0.98095,0.94264,0.999363,0.965444,1,0.999409,0.979753,0.82103,0.99997,1,0.40729,1,0.9993,0.999782,0.99884,0.999999,0.909474,0.916791,0.713807,1,0.983726,1,0.999989,0.98908,0.159898,0.999406,0.992737,0.0621435,0.984045,0.999914,0.172967,1,0.999736,1,0.999082,0.996987,0.614487,0.98677,1,0.997404,0.99036,0.99833,0.999943,0.997156,1,0.999582,0.9907,0.68838,1,0.99789,0.99926,0.999997,0.999186,0.999969,1,1,0.998925,0.996278,0.994048,0.997117,0.996994,0.999989,0.99601,0.994118,0.990777,0.999945,1,0.999999,0.999997,1,0.999923,0.999999,0.882326,1,0.36264,0.999586,0.944166,0.990245,0.0784107,1,0.999858,0.999774,0.563712,0.633302,0.999467,0.999684,1,1,0.98759,0.99379,0.231596,0.99884,0.989804,0.998321,0.998958,0.999822,0.982852,0.855498,0.999681,0.937958,1,0.978229,0.9588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| ||
}} | }} |
Revision as of 14:26, 19 October 2012
Full id: C28_thymus_acute_vein_Hodgkin_chronic_throat_Dendritic
Phase1 CAGE Peaks
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
p.value | FDR | nGenes | nPathway | Name |
---|---|---|---|---|
6.54052691149315e-09 | 4.14015353497516e-06 | 7 | 88 | Hematopoietic cell lineage (KEGG):04640 |
3.09376651138622e-06 | 0.000652784733902493 | 4 | 35 | Primary immunodeficiency (KEGG):05340 |
4.16631468269243e-05 | 0.00659319298536076 | 5 | 133 | T Cell Receptor Signaling Pathway (Wikipathways):WP69 |
0.000209864686631542 | 0.0265688693275532 | 6 | 295 | IL-2 down reg. targets (Netpath):NetPath_14 |
3.66016971681764e-07 | 0.000115844371537278 | 5 | 51 | {HLA-A,53} (Static Module):NA |
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 ID | GO name | FDR corrected p-value |
---|---|---|
GO:0005886 | plasma membrane | 2.58863273738666e-07 |
GO:0005887 | integral to plasma membrane | 0.000403900771274977 |
GO:0031226 | intrinsic to plasma membrane | 0.000403900771274977 |
GO:0044459 | plasma membrane part | 0.00106010826523271 |
GO:0033151 | V(D)J recombination | 0.00141588626863272 |
GO:0002376 | immune system process | 0.00141588626863272 |
GO:0046649 | lymphocyte activation | 0.00141588626863272 |
GO:0045321 | leukocyte activation | 0.00254385803382731 |
GO:0042110 | T cell activation | 0.00340439395997296 |
GO:0001775 | cell activation | 0.00414532562306431 |
GO:0006955 | immune response | 0.00642667675818567 |
GO:0044425 | membrane part | 0.0139590338276538 |
GO:0042101 | T cell receptor complex | 0.0139590338276538 |
GO:0030098 | lymphocyte differentiation | 0.0143426469860848 |
GO:0007165 | signal transduction | 0.014806169332634 |
GO:0007154 | cell communication | 0.014806169332634 |
GO:0016021 | integral to membrane | 0.014806169332634 |
GO:0016444 | somatic cell DNA recombination | 0.014806169332634 |
GO:0002562 | somatic diversification of immune receptors via germline recombination within a single locus | 0.014806169332634 |
GO:0032501 | multicellular organismal process | 0.014806169332634 |
GO:0031224 | intrinsic to membrane | 0.014806169332634 |
GO:0002200 | somatic diversification of immune receptors | 0.0149222207183145 |
GO:0001772 | immunological synapse | 0.0161562729408093 |
GO:0050885 | neuromuscular process controlling balance | 0.0173966484463092 |
GO:0003002 | regionalization | 0.0192712148806265 |
GO:0044464 | cell part | 0.0192712148806265 |
GO:0002521 | leukocyte differentiation | 0.0202283749230182 |
GO:0050905 | neuromuscular process | 0.0245033491211059 |
GO:0019882 | antigen processing and presentation | 0.0323364339259782 |
GO:0043235 | receptor complex | 0.0323364339259782 |
GO:0030183 | B cell differentiation | 0.0323364339259782 |
GO:0016020 | membrane | 0.0323364339259782 |
GO:0044424 | intracellular part | 0.0323364339259782 |
GO:0007389 | pattern specification process | 0.0323364339259782 |
GO:0005622 | intracellular | 0.0323364339259782 |
GO:0030290 | sphingolipid activator protein activity | 0.0323364339259782 |
GO:0045023 | G0 to G1 transition | 0.0323364339259782 |
GO:0032428 | beta-N-acetylgalactosaminidase activity | 0.0323364339259782 |
GO:0060123 | regulation of growth hormone secretion | 0.0323364339259782 |
GO:0021542 | dentate gyrus development | 0.0323364339259782 |
GO:0031770 | growth hormone-releasing hormone receptor binding | 0.0323364339259782 |
GO:0050429 | calcium-dependent phospholipase C activity | 0.0323364339259782 |
GO:0032236 | positive regulation of calcium ion transport via store-operated calcium channel | 0.0323364339259782 |
GO:0060124 | positive regulation of growth hormone secretion | 0.0323364339259782 |
GO:0032237 | activation of store-operated calcium channel activity | 0.0323364339259782 |
GO:0048736 | appendage development | 0.0362183100820045 |
GO:0060173 | limb development | 0.0362183100820045 |
GO:0035107 | appendage morphogenesis | 0.0362183100820045 |
GO:0035108 | limb morphogenesis | 0.0362183100820045 |
GO:0007167 | enzyme linked receptor protein signaling pathway | 0.0418667281225795 |
GO:0030217 | T cell differentiation | 0.0426044283894715 |
GO:0065007 | biological regulation | 0.0426044283894715 |
GO:0032502 | developmental process | 0.0426044283894715 |
GO:0030097 | hemopoiesis | 0.0426044283894715 |
GO:0001550 | ovarian cumulus expansion | 0.0426044283894715 |
GO:0005889 | hydrogen:potassium-exchanging ATPase complex | 0.0426044283894715 |
GO:0000301 | retrograde transport, vesicle recycling within Golgi | 0.0426044283894715 |
GO:0022605 | oogenesis stage | 0.0426044283894715 |
GO:0016004 | phospholipase activator activity | 0.0426044283894715 |
GO:0001547 | antral ovarian follicle growth | 0.0426044283894715 |
GO:0045179 | apical cortex | 0.0426044283894715 |
GO:0032234 | regulation of calcium ion transport via store-operated calcium channel | 0.0426044283894715 |
GO:0048165 | fused antrum stage, oogenesis | 0.0426044283894715 |
GO:0000042 | protein targeting to Golgi | 0.0426044283894715 |
GO:0043270 | positive regulation of ion transport | 0.0426044283894715 |
GO:0000320 | re-entry into mitotic cell cycle | 0.0426044283894715 |
GO:0009313 | oligosaccharide catabolic process | 0.0426044283894715 |
GO:0051928 | positive regulation of calcium ion transport | 0.0426044283894715 |
GO:0004871 | signal transducer activity | 0.0426044283894715 |
GO:0060089 | molecular transducer activity | 0.0426044283894715 |
GO:0048534 | hemopoietic or lymphoid organ development | 0.0495232595679893 |
GO:0030176 | integral to endoplasmic reticulum membrane | 0.0499901260683767 |
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><br>uberon_data<br><br>
Ontology term | p-value | n |
---|---|---|
hemopoietic organ | 6.03e-43 | 7 |
immune organ | 6.03e-43 | 7 |
thymus | 4.28e-34 | 4 |
hemolymphoid system gland | 4.28e-34 | 4 |
thymic region | 4.28e-34 | 4 |
pharyngeal gland | 4.28e-34 | 4 |
thymus primordium | 4.28e-34 | 4 |
neck | 1.86e-30 | 10 |
pharyngeal epithelium | 3.88e-23 | 6 |
throat | 9.07e-18 | 2 |
gland of gut | 2.49e-14 | 10 |
chordate pharynx | 2.49e-14 | 10 |
pharyngeal region of foregut | 2.49e-14 | 10 |
pharynx | 4.00e-13 | 11 |
entire pharyngeal arch endoderm | 4.00e-13 | 11 |
early pharyngeal endoderm | 4.00e-13 | 11 |
spleen | 3.24e-12 | 3 |
gastrointestinal system mesentery | 3.24e-12 | 3 |
stomach region | 3.24e-12 | 3 |
mesentery | 3.24e-12 | 3 |
gastrointestinal system serosa | 3.24e-12 | 3 |
mesentery of stomach | 3.24e-12 | 3 |
gut mesentery | 3.24e-12 | 3 |
dorsal mesentery | 3.24e-12 | 3 |
dorsal mesogastrium | 3.24e-12 | 3 |
peritoneal cavity | 3.24e-12 | 3 |
spleen primordium | 3.24e-12 | 3 |
mixed endoderm/mesoderm-derived structure | 4.97e-11 | 29 |
pharyngeal arch system | 2.09e-08 | 18 |
upper respiratory tract | 5.16e-08 | 19 |
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) |
---|---|
{{{tfbs_overrepresentation_jaspar}}} |
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
No analysis results for this cluster
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