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	red	network_comparison	green

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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	red	network_comparison	green
mad protein (max dimerizer). [swissprot;acc:q05195]	253	228	1.11583	204.333
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	228.513	1.01956	232.983
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368]	2088	218.124	1.00781	216.433
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5]	1479	228.469	1.0192	232.855
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	238.529	1.06528	254.099
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	954	267.447	1.03487	276.773
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	1634	215.772	1.01494	212.596
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	219.306	1.01766	223.179
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	929	225.955	1.03642	218.015
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	15	1.86667	28
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	1267	171.231	1.02425	167.177
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650]	922	236.741	1.0372	245.547
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	224.244	1.04578	234.511
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	508	177.698	1.07058	190.24
mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]	2411	194.407	1.00362	193.706
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	259	227.999	1.11562	204.37
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	256		1.11569	204.357
max protein. [swissprot;acc:p25912]	425	227.828	1.082	210.561
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	258	227.999	1.11564	204.366
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	2331	229.258	1.00452	230.294
mct-1 protein. [refseq;acc:nm_014060]	486	226.313	1.07387	243.03
megf10 protein. [refseq;acc:nm_032446]	1944	224.341	1.00987	222.148
megf11 protein. [refseq;acc:nm_032445]	1943	224.34		222.147
megf6 (fragment). [sptrembl;acc:o75095]	1756	221.811	1.01242	219.09
megsin (tp55) (serpin b7). [swissprot;acc:o75635]	2414	218.2	1.00359	218.984
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	2259	213.391	1.00569	214.606
meiotic recombination protein spo11. [swissprot;acc:q9y5k1]	924	236.741	1.0372	245.547
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	816	212.386	1.04425	221.785
melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]	2495	194.527	1.00284	195.08
melanoma antigen, family b, 6. [refseq;acc:nm_173523]	93	88.2482	1.24949	110.265
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.