MK5 Microarray Data

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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Value Type	Network Comparison Type	Gene	description	Rank	Filtered	Interaction Map	green	network_comparison	red

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Showing element 1580 to 1629 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence

description	Rank	green	network_comparison	red
mad protein (max dimerizer). [swissprot;acc:q05195]	253	204.333	1.11583	228
mago nashi protein homolog. [swissprot;acc:p50606]	2864	0.00001	1	0.00001
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	1467	232.983	1.01956	228.513
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368]	2088	216.433	1.00781	218.124
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5]	1479	232.855	1.0192	228.469
major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]	3013	0.00001	1	0.00001
malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925]	3213
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	571	254.099	1.06528	238.529
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	954	276.773	1.03487	267.447
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	1634	212.596	1.01494	215.772
mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487]	3070	0.00001	1	0.00001
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949]	1522	223.179	1.01766	219.306
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	929	218.015	1.03642	225.955
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	2	28	1.86667	15
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	1267	167.177	1.02425	171.231
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650]	922	245.547	1.0372	236.741
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]	923
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	792	234.511	1.04578	224.244
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	508	190.24	1.07058	177.698
mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]	2411	193.706	1.00362	194.407
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	259	204.37	1.11562	227.999
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	256	204.357	1.11569
max protein. [swissprot;acc:p25912]	425	210.561	1.082	227.828
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	258	204.366	1.11564	227.999
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	2331	230.294	1.00452	229.258
mct-1 protein. [refseq;acc:nm_014060]	486	243.03	1.07387	226.313
megf10 protein. [refseq;acc:nm_032446]	1944	222.148	1.00987	224.341
megf11 protein. [refseq;acc:nm_032445]	1943	222.147		224.34
megf6 (fragment). [sptrembl;acc:o75095]	1756	219.09	1.01242	221.811
megsin (tp55) (serpin b7). [swissprot;acc:o75635]	2414	218.984	1.00359	218.2
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	2259	214.606	1.00569	213.391
meiotic recombination protein spo11. [swissprot;acc:q9y5k1]	924	245.547	1.0372	236.741
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	816	221.785	1.04425	212.386
melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]	2495	195.08	1.00284	194.527
melanoma antigen, family b, 6. [refseq;acc:nm_173523]	93	110.265	1.24949	88.2482
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	83
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	99
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	100
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	86
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	98
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	87
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	85
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	94
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	89
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	96
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	95
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	101
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	97
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	91
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	102

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.