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

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Showing element 501 to 550 of 77072 in total

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Rank	Value Type	green	description	Network Comparison Type	network_comparison	Interaction Map	red
32	Ranked	8691.76	importin 9. [refseq;acc:nm_018085]	Divided	1.52929	High confidence	13292.2
		14842.4	pnas-129. [sptrembl;acc:q9bxv8]	Subtracted	3734.8	Low confidence	11107.6
		15983.3	myoglobin. [swissprot;acc:p02144]	Divided	1.39162		11485.4
		19014.6	syntaxin 10 (syn10). [swissprot;acc:o60499]	Subtracted	5130.2	High confidence	13884.4
	Squared	0.355148	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Divided	9.62112	Low confidence	3.41692
		4.57302	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]		16.8159	High confidence	76.8994
		27221.2	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	Subtracted	7328.6		19892.6
		48048.2	myosin regulatory light chain 2, nonsarcomeric (myosin rlc). [swissprot;acc:p19105]		6799.3	Low confidence	54847.5
	Rooted	5.80678	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Divided	1.69589		9.84765
		9.43398	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Subtracted	9.43398	High confidence	0
		11.258	ubiquitin protein ligase. [refseq;acc:nm_130466]	Divided	2.13529		24.0391
		47.9266	fibrillin 3. [refseq;acc:nm_032447]	Subtracted	6.8075	Low confidence	54.7341
33	Measured	35.5	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Divided	2.97183		105.5
		39.8063	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]		3.15402	High confidence	12.6208
		4245.16	scribble. [refseq;acc:nm_015356]	Subtracted	547.36	Low confidence	3697.8
		9192.38	protein cgi-147. [swissprot;acc:q9y3e5]		796.26	High confidence	8396.12
	Ranked	7867	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]		3648	Low confidence	11515
		8691.76	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Divided	1.52929	High confidence	13292.2
		14746.1	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]		1.37827	Low confidence	20324.1
		20387	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Subtracted	5123	High confidence	15264
	Squared	0.355148	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Divided	9.62112	Low confidence	3.41692
		4.57302	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]		16.8159	High confidence	76.8994
		36822.7	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Subtracted	7010.7		29812
		130587	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]		6603	Low confidence	123984
	Rooted	5.80678	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Divided	1.69589		9.84765
		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]		2.0801	High confidence	12.3693
		58.122	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Subtracted	6.5363	Low confidence	64.6583
		70.9983	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]		9.359	High confidence	61.6393
34	Measured	35.5	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Divided	2.97183	Low confidence	105.5
		47	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]		3.04255	High confidence	143
		1361.92	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Subtracted	521.18	Low confidence	840.74
		3340.03	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]		791.03	High confidence	4131.06
	Ranked	6812	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]		4731		11543
		7506.66	fibrillin 3. [refseq;acc:nm_032447]	Divided	1.37724	Low confidence	5450.5
		9520.8	sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8]	Subtracted	3531.9		13052.7
		17173.8	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Divided	1.52196	High confidence	11284
	Squared	0.355148	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		9.62112	Low confidence	3.41692
		0.697197	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]		15.9968	High confidence	0.0435834
		72701	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Subtracted	6682.4		79383.4
		129956	th1-like; th1 drosophila homolog; th1-like (drosophila homolog); negative elongation factor proteins c and d. [refseq;acc:nm_016397]		6596	Low confidence	136552
	Rooted	5.80678	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Divided	1.69589		9.84765
		11.7898	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]		2.02503	High confidence	23.8747
		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]	Subtracted	9.32772		3.16228
		14.4058	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]		6.50517	Low confidence	7.90063
35	Measured	35.5	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Divided	2.97183		105.5
		662	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Subtracted	509		153
		898	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]		705	High confidence	1603
		1377	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Divided	2.99674		459.5
	Ranked	4871.6	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		1.5182		3208.8
		8691.76	importin 9. [refseq;acc:nm_018085]	Subtracted	4600.44		13292.2

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.