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

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Showing element 1608 to 1657 of 3228 in total

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

description	Rank	network_comparison	green	red
megf6 (fragment). [sptrembl;acc:o75095]	1756	1.01242	219.09	221.811
megsin (tp55) (serpin b7). [swissprot;acc:o75635]	2414	1.00359	218.984	218.2
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	2259	1.00569	214.606	213.391
meiotic recombination protein spo11. [swissprot;acc:q9y5k1]	924	1.0372	245.547	236.741
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	816	1.04425	221.785	212.386
melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]	2495	1.00284	195.08	194.527
melanoma antigen, family b, 6. [refseq;acc:nm_173523]	93	1.24949	110.265	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
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	92
membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792]	2589	1.0015	212.422	212.74
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835]	1393	1.02148	213.875	218.47
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]	533	1.06782	235.004	250.942
membrane-bound transcription factor site 2 protease (ec 3.4.24.-) (site-2 protease) (sterol-regulatory element-binding proteins intramembrane protease). [swissprot;acc:o43462]	3215	1	0.00001	0.00001
mesoderm induction early response 1. [refseq;acc:nm_020948]	2426	1.00357	211.618	212.374
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416]	2558	1.00175	223.047	222.658
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	2559
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	300	1.10196	166.351	150.959
metastasis-associated protein mta1. [swissprot;acc:q13330]	280	1.10578	228.356	252.512
metaxin 1. [swissprot;acc:q13505]	1151	1.02693	204.925	199.552
metaxin 2. [swissprot;acc:o75431]	517	1.06949	234.793	219.537
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	314	1.10027	268.604	244.126
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	315
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5]	2325	1.00473	220.685	221.728
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	648	1.05895	206.078	218.227
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]	2434	1.00346	212.286	213.021
methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252]	1962	1.00978	213.702	211.632
methyltransferase like 2. [refseq;acc:nm_018396]	846	1.04184	153.371	147.211
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	725	1.0526	247.673	235.296
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	38	1.27273	253	322
microfibrillar-associated protein 1. [swissprot;acc:p55081]	2949	1	0.00001	0.00001
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	927	1.03713	210.139	217.942
microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]	754	1.04968	235.583	224.434
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	448	1.07822	246.338	228.468
microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]	602	1.06069	218.792	206.274
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]	2719	1.00052	216.632	216.52
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]	2720		216.633

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.