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

Results: HTML CSV LaTeX

Showing element 1 to 32 of 32 in total

Rank  : 22

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