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 6041 to 6090 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
1511 Measured serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] 7234.61 7771.58 1.07422
Ranked cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 213.268 209.509 1.01794
Squared oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] 14522.9 16175.3 1.11378
Rooted nucleoporin like 1. [refseq;acc:nm_014089] 63.302 65.6446 1.03701
1512 Measured sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] 7234.61 7771.58 1.07422
Ranked surfeit locus protein 1. [swissprot;acc:q15526] 213.268 209.509 1.01794
Squared senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 14522.9 16175.3 1.11378
Rooted rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] 63.302 65.6446 1.03701
1513 Measured 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
Ranked cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] 213.268 209.509 1.01794
Squared oligophrenin 1. [swissprot;acc:o60890] 14522.9 16175.3 1.11378
Rooted cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] 63.302 65.6446 1.03701
1514 Measured 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
Ranked protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] 213.268 209.509 1.01794
Squared guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 2547.12 2286.96 1.11376
Rooted 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 63.609 65.9615 1.03698
1515 Measured 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
Ranked dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 213.267 209.511 1.01793
Squared guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 2547.12 2286.96 1.11376
Rooted af-6 protein. [swissprot;acc:p55196] 61.7453 64.0287 1.03698
1516 Measured 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] 5633.67 6050.69 1.07402
Ranked dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 213.267 209.511 1.01793
Squared putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] 21282.4 23701.9 1.11369
Rooted adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 63.0853 65.4141 1.03692
1517 Measured 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] 5996.14 6439.46 1.07393
Ranked seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] 213.267 209.511 1.01793
Squared rho interacting protein 3. [refseq;acc:nm_015134] 24157.2 26903.5 1.11368
Rooted traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] 61.9527 64.2401 1.03692
1518 Measured anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] 10341.2 9630.35 1.07381
Ranked [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] 213.259 209.524 1.01783
Squared protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] 24156 26902 1.11368
Rooted nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 62.4888 64.793 1.03687
1519 Measured gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 5283.8 5673.81 1.07381
Ranked cone-rod homeobox protein. [swissprot;acc:o43186] 244.331 240.061 1.01779
Squared mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] 28609.1 31855 1.11346
Rooted vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] 63.2569 65.5867 1.03683
1520 Measured gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] 5283.8 5673.81 1.07381
Ranked homeobox protein otx1. [swissprot;acc:p32242] 244.367 240.098 1.01778
Squared ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] 28606.2 31850.3 1.11341
Rooted vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] 63.2569 65.5867 1.03683
1521 Measured 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] 5938.56 6376.76 1.07379
Ranked homeobox protein otx2. [swissprot;acc:p32243] 244.478 240.212 1.01776
Squared calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] 28606.2 31850.3 1.11341
Rooted vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] 63.2569 65.5867 1.03683
1522 Measured 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
Ranked mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 219.306 223.179 1.01766
Squared calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] 28606.2 31850.3 1.11341
Rooted protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] 62.1861 64.4641 1.03663
1523 Measured glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 6137.09 6589.57 1.07373
Ranked putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] 219.306 223.179 1.01766

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/