Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2012 to 2061 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
503 Rooted nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 177.987 194.29 1.0916
504 Measured enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 10067.9 11511 1.14334
Ranked oligophrenin 1. [swissprot;acc:o60890] 238.704 255.68 1.07112
Squared vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] 30286.5 36362 1.2006
Rooted ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 144.606 157.824 1.09141
505 Measured signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 6856.71 7838.3 1.14316
Ranked ad24 protein. [refseq;acc:nm_022451] 251.334 234.672 1.071
Squared protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] 30286.5 36362 1.2006
Rooted ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 144.606 157.824 1.09141
506 Measured eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 3893.85 4450.98 1.14308
Ranked inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] 224.535 240.476 1.071
Squared vav-2 protein. [swissprot;acc:p52735] 31377.3 37670.1 1.20055
Rooted ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 144.606 157.824 1.09141
507 Measured cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 6875.08 7858.38 1.14302
Ranked wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 251.299 234.729 1.07059
Squared puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] 23512.2 28206.2 1.19964
Rooted anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 144.606 157.824 1.09141
508 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 7556.75 8636.87 1.14293
Ranked mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 177.698 190.24 1.07058
Squared leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] 23512.2 28206.2 1.19964
Rooted autoantigen ngp-1. [swissprot;acc:q13823] 49.4756 53.9896 1.09124
509 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 7551.8 8630.06 1.14278
Ranked carboxypeptidase b precursor. [refseq;acc:nm_020361] 177.698 190.239 1.07057
Squared dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] 23512.2 28206.2 1.19964
Rooted 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 50.2583 46.057 1.09122
510 Measured growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 5975.11 6826.24 1.14245
Ranked plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 177.699 190.24 1.07057
Squared transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 17281.7 20723 1.19913
Rooted protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 149.397 136.972 1.09071
511 Measured serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] 5975.11 6826.24 1.14245
Ranked proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 250.053 233.725 1.06986
Squared nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 17281.7 20723 1.19913
Rooted suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 50.5979 46.392 1.09066
512 Measured small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 10807.4 12338.5 1.14167
Ranked block of proliferation 1. [swissprot;acc:q14137] 250.794 234.433 1.06979
Squared cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 19987.6 23960.7 1.19878
Rooted protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 56.3798 61.4858 1.09056
513 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 7485.08 8543.66 1.14143
Ranked segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 218.596 204.344 1.06975
Squared transforming protein rhoc (h9). [swissprot;acc:p08134] 19987.6 23960.7 1.19878
Rooted 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 51.5881 47.3127 1.09036
514 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 7477 8532.02 1.1411
Ranked segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 218.613 204.382 1.06963
Squared thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 19987.6 23960.7 1.19878
Rooted xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 58.7805 64.0772 1.09011
515 Measured transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 3890.53 4439.07 1.14099
Ranked pescadillo homolog 1. [swissprot;acc:o00541] 251.297 234.941 1.06962
Squared 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 19987.6 23960.7 1.19878
Rooted u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 56.3551 61.4322 1.09009
516 Measured n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 4910.6 5600.61 1.14051

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/