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

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Showing element 273 to 322 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Ranked	Divided	1	185.678	245.247	1.32082
	60s ribosomal protein l37a. [swissprot;acc:p12751]	Measured		0	305.45	26.1599	11.6763
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Squared			439.709	0.52284	841.001
	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Measured	Subtracted		15411.3	14167	1244.3
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Rooted	Divided		9.20014	60.0707	6.52932
	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Squared	Subtracted		43393.5	56658.6	13265.1
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Rooted		1	203.673	182.638	21.035
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		Divided		21.4476	36.9459	1.72261
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Ranked	Subtracted	0	7509.39	14178.1	6668.71
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]			1	266.865	336.181	69.316
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Divided	0	22286	13216	1.68629
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Squared	Subtracted	1	219048	129762	89286
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Measured			24255.7	18168.9	6086.8
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]		Divided		677.5	1865.5	2.75351
		Squared			108.641	823.69	7.58176
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Rooted	Subtracted	0	12.4097	0	12.4097
19	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Measured	Divided		305.45	26.1599	11.6763
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]		Subtracted	1	24250	18164.9	6085.1
	cytohesin 4. [swissprot;acc:q9uia0]	Rooted			203.673	182.638	21.035
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Measured		0	1593	2804	1211
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Ranked	Divided	1	185.678	245.247	1.32082
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]		Subtracted		266.865	336.178	69.313
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		Divided	0	22286	13216	1.68629
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Rooted			9.20014	60.0707	6.52932
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Squared	Subtracted	1	219048	129762	89286
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Measured	Divided		677.5	1865.5	2.75351
		Squared			108.641	823.69	7.58176
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Ranked	Subtracted	0	4475.84	11083.9	6608.06
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Squared			10489.8	23426.5	12936.7
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Rooted			23.8747	11.7898	12.0849
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]		Divided	1	25.6987	43.561	1.69507
	serpin b12. [swissprot;acc:q96p63]	Squared		0	23.5744	0.0289898	813.196
20	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Rooted	Subtracted		23.8747	11.7898	12.0849
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]		Divided		11.3774	1.80368	6.30788
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		Subtracted	1	203.673	182.638	21.035
	ero1-like. [refseq;acc:nm_014584]	Measured	Divided	0	82	0.00001	8200000
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]		Subtracted	1	23421.5	17580.4	5841.1
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Ranked	Divided		185.678	245.247	1.32082
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]		Subtracted		266.868	336.159	69.291
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Rooted	Divided		40.3337	24.2744	1.66157
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Ranked		0	22286	13216	1.68629
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Squared			23.4957	0.0297673	789.312
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]		Subtracted	1	219048	129762	89286
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Measured		0	8763	7608	1155
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]		Divided	1	677.5	1865.5	2.75351
		Squared			108.641	823.69	7.58176
	serpin b12. [swissprot;acc:q96p63]	Ranked	Subtracted	0	14604.2	21138.6	6534.4
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Squared			38799.5	25982	12817.5
21	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	Ranked	Divided		6313.38	10621.4	1.68236
		Rooted	Subtracted		44.2946	32.7593	11.5353

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.