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

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Showing element 1610 to 1659 of 3228 in total

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

description	Rank	red	green	network_comparison
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
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	212.74	212.422	1.0015
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835]	1393	218.47	213.875	1.02148
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]	533	250.942	235.004	1.06782
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	0.00001	0.00001	1
mesoderm induction early response 1. [refseq;acc:nm_020948]	2426	212.374	211.618	1.00357
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416]	2558	222.658	223.047	1.00175
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	2559
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	300	150.959	166.351	1.10196
metastasis-associated protein mta1. [swissprot;acc:q13330]	280	252.512	228.356	1.10578
metaxin 1. [swissprot;acc:q13505]	1151	199.552	204.925	1.02693
metaxin 2. [swissprot;acc:o75431]	517	219.537	234.793	1.06949
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	314	244.126	268.604	1.10027
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	221.728	220.685	1.00473
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	648	218.227	206.078	1.05895
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]	2434	213.021	212.286	1.00346
methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252]	1962	211.632	213.702	1.00978
methyltransferase like 2. [refseq;acc:nm_018396]	846	147.211	153.371	1.04184
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	725	235.296	247.673	1.0526
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	38	322	253	1.27273
microfibrillar-associated protein 1. [swissprot;acc:p55081]	2949	0.00001	0.00001	1
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	927	217.942	210.139	1.03713
microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]	754	224.434	235.583	1.04968
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	448	228.468	246.338	1.07822
microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]	602	206.274	218.792	1.06069
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]	2719	216.52	216.632	1.00052
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]	2720		216.633
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	2717	216.521	216.634
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	16	56.7252	75.3954	1.32913

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.