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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1480 to 1529 of 3228 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
green
network_comparison
1480 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 5660.17 6085.22 1.07509
1481 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 3688.8 3431.33 1.07504
1482 leng5 protein. [refseq;acc:nm_024075] 5372.25 5775.21 1.07501
1483 tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381]
1484 ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]
1485 tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6]
1486 thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]
1487 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] 5573.64 5991.58 1.07499
1488 delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886]
1489 vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] 6192.38 6656.34 1.07492
1490 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] 6340.5 6815.41 1.0749
1491 fidgetin-like 1. [refseq;acc:nm_022116] 6057.46 6510.9 1.07486
1492 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] 4619.81 4965.45 1.07482
1493 deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] 6146.36 6606.21
1494 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] 4619.81 4965.45
1495 nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] 6362.92 6838.6 1.07476
1496 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 5945.56 6389.63 1.07469
1497 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 6339.08 6812.45 1.07467
1498 40s ribosomal protein s13. [swissprot;acc:q02546] 5414.98 5818.7 1.07456
1499 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 5798.31 6230.55 1.07455
1500 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 10075.5 9377.75 1.0744
1501 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
1502 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]
1503 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]
1504 peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]
1505 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
1506 hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] 6152.78 6610.46 1.07439
1507 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]
1508 guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3]
1509 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 7237.39 7775.21 1.07431
1510 60s ribosomal protein l21. [swissprot;acc:p46778] 5546.11 5957.99 1.07426
1511 serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] 7234.61 7771.58 1.07422
1512 sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312]
1513 proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] 6079.65 6530.82 1.07421
1514 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 7232.14 7768.35 1.07414
1515 lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] 5633.67 6050.69 1.07402
1516 lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055]
1517 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] 5996.14 6439.46 1.07393
1518 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] 10341.2 9630.35 1.07381
1519 gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 5283.8 5673.81
1520 gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335]
1521 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] 5938.56 6376.76 1.07379
1522 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] 6137.24 6589.72 1.07373
1523 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 6137.09 6589.57
1524 glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 6137.53 6590.01 1.07372
1525 tensin. [refseq;acc:nm_022648] 5871.89 6303.56 1.07351
1526 calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 5369.1 5763.72 1.0735
1527 26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] 5926.76 6362.33 1.07349
1528 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 5869.97 6301.24 1.07347
1529 dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] 5916.05 6350.53 1.07344

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/