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

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Showing element 1575 to 1624 of 3228 in total

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

description	Rank	red	green	network_comparison
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304]	1343	258.558	252.916	1.02231
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]	1642	260.269	256.531	1.01457
m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307]	1504	259.439	254.797	1.01822
mab-21-like protein 1; mab-21-like 1. [refseq;acc:nm_005584]	2786	0.00001	0.00001	1
mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439]	2783
mad protein (max dimerizer). [swissprot;acc:q05195]	253	228	204.333	1.11583
mago nashi protein homolog. [swissprot;acc:p50606]	2864	0.00001	0.00001	1
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	1467	228.513	232.983	1.01956
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368]	2088	218.124	216.433	1.00781
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5]	1479	228.469	232.855	1.0192
major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]	3013	0.00001	0.00001	1
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	254.099	1.06528
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	276.773	1.03487
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	1634	215.772	212.596	1.01494
mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487]	3070	0.00001	0.00001	1
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949]	1522	219.306	223.179	1.01766
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	929	225.955	218.015	1.03642
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	28	1.86667
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	167.177	1.02425
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650]	922	236.741	245.547	1.0372
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	234.511	1.04578
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	508	177.698	190.24	1.07058
mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]	2411	194.407	193.706	1.00362
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	259	227.999	204.37	1.11562
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	256		204.357	1.11569
max protein. [swissprot;acc:p25912]	425	227.828	210.561	1.082
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	258	227.999	204.366	1.11564
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	2331	229.258	230.294	1.00452
mct-1 protein. [refseq;acc:nm_014060]	486	226.313	243.03	1.07387
megf10 protein. [refseq;acc:nm_032446]	1944	224.341	222.148	1.00987
megf11 protein. [refseq;acc:nm_032445]	1943	224.34	222.147
megf6 (fragment). [sptrembl;acc:o75095]	1756	221.811	219.09	1.01242
megsin (tp55) (serpin b7). [swissprot;acc:o75635]	2414	218.2	218.984	1.00359
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	2259	213.391	214.606	1.00569
meiotic recombination protein spo11. [swissprot;acc:q9y5k1]	924	236.741	245.547	1.0372
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	816	212.386	221.785	1.04425
melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]	2495	194.527	195.08	1.00284
melanoma antigen, family b, 6. [refseq;acc:nm_173523]	93	88.2482	110.265	1.24949
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

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.