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

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Showing element 1 to 32 of 32 in total

Rank  : 22

Interaction Map	Value Type	Filtered	green	description	red	Network Comparison Type	network_comparison
High confidence	Measured	0	0.00001	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60	Divided	6000000
			30022.4	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	31122	Subtracted	1099.6
		1	1865.5	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	677.5	Divided	2.75351
			18263	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	23693.7	Subtracted	5430.7
	Ranked	0	11965.7	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	5510.5		6455.2
			12479	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	20989	Divided	1.68195
		1	245.247	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	185.678		1.32082
			253	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	322	Subtracted	69
	Squared	0	0.0532544	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	0.000236686	Divided	225
			204096	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	192242	Subtracted	11854
		1	823.69	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	108.641	Divided	7.58176
			129762	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	219048	Subtracted	89286
	Rooted	0	12.49	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	3.16228	Divided	3.94968
			13.5647	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	24.454	Subtracted	10.8893
		1	24.2915	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	40.3357	Divided	1.66049
			133.176	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	153.578	Subtracted	20.402
Low confidence	Measured	0	0.00001	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	37	Divided	3700000
			4100.24	sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796]	4821.65	Subtracted	721.41
		1	543.5	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	2399.5		1856
			3997.02	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	3126.88	Divided	1.27828
	Ranked	0	7597.61	adenomatous polyposis coli like. [refseq;acc:nm_005883]	12074.1	Subtracted	4476.49
			7867	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	11515	Divided	1.46371
		1	163	n33 protein. [swissprot;acc:q13454]	198		1.21472
			246.125	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	210.241	Subtracted	35.884
	Squared	0	0.697197	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	0.0435834	Divided	15.9968
			78378.5	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	70246.6	Subtracted	8131.9
		1	57685.7	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	80340.8	Divided	1.39273
			159767	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	122475	Subtracted	37292
	Rooted	0	1.2188	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	10.3085		9.0897
			25.7294	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	12.3693	Divided	2.0801
		1	71.1231	implantation-associated protein. [refseq;acc:nm_032121]	57.2538		1.24224
				n33 protein. [swissprot;acc:q13454]		Subtracted	13.8693

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.