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

Results: HTML CSV LaTeX

Showing element 551 to 600 of 77072 in total

Rank	Filtered	description	green	Value Type	Network Comparison Type	red	network_comparison	Interaction Map
18	0	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	19	Measured	Divided	99	5.21053	Low confidence
		clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	56658.6	Squared	Subtracted	43393.5	13265.1	High confidence
		early hematopoietic zinc finger. [refseq;acc:nm_015461]	8903.28	Ranked	Divided	5850.23	1.52187	Low confidence
		elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9]	11505		Subtracted	16116.4	4611.4
		fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	14178.1			7509.39	6668.71	High confidence
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	13216		Divided	22286	1.68629
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	9.43398	Rooted	Subtracted	0	9.43398	Low confidence
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	58	Measured		859	801
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	Rooted		12.4097	12.4097	High confidence
		ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	18724.4	Squared		9955.21	8769.19	Low confidence
	1	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	245.247	Ranked	Divided	185.678	1.32082	High confidence
		cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	7251	Measured		5492.04	1.32027	Low confidence
		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	182.638	Rooted	Subtracted	203.673	21.035	High confidence
		dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	36.9459		Divided	21.4476	1.72261
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	336.181	Ranked	Subtracted	266.865	69.316
		homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	17572.7	Measured		15464.1	2108.6	Low confidence
		homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	159767	Squared		122475	37292
		jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	247.169	Ranked	Divided	305.303	1.2352
		melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	129762	Squared	Subtracted	219048	89286	High confidence
		microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	18168.9	Measured		24255.7	6086.8
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	473408	Squared	Divided	332411	1.42416	Low confidence
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	55.937	Rooted		44.4168	1.25937
			232.49	Ranked	Subtracted	273.188	40.698
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	823.69	Squared	Divided	108.641	7.58176	High confidence
			1865.5	Measured		677.5	2.75351
		trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	47.928	Rooted	Subtracted	32.2231	15.7049	Low confidence
19	0	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]	26.1599	Measured	Divided	305.45	11.6763	High confidence
		alpha 2 globin. [refseq;acc:nm_000517]	15987.1	Ranked	Subtracted	11486.2	4500.9	Low confidence
		dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2804	Measured		1593	1211	High 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]	662		Divided	153	4.3268	Low confidence
		fos-related antigen 2. [swissprot;acc:p15408]	2407.27		Subtracted	3205.98	798.71
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	9.43398	Rooted		0	9.43398
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	13216	Ranked	Divided	22286	1.68629	High confidence
		l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338]	8.50775	Rooted		3.94084	2.15887	Low confidence
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	60.0707			9.20014	6.52932	High confidence
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	Ranked	Subtracted	4475.84	6608.06
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	4871.6		Divided	3208.8	1.5182	Low confidence
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	23426.5	Squared	Subtracted	10489.8	12936.7	High confidence
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	11.7898	Rooted		23.8747	12.0849
		potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	141.944	Squared	Divided	6.25494	22.6931	Low confidence
		serpin b12. [swissprot;acc:q96p63]	0.0289898			23.5744	813.196	High confidence
		succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	133193		Subtracted	124602	8591	Low confidence
	1	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]	3915.4	Measured	Divided	3032.56	1.29112
		cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	18164.9		Subtracted	24250	6085.1	High confidence
		cytohesin 4. [swissprot;acc:q9uia0]	182.638	Rooted		203.673	21.035
		glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	245.247	Ranked	Divided	185.678	1.32082
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	336.178		Subtracted	266.865	69.313
		histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773]	228.509			188.298	40.211	Low confidence
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	17572.7	Measured		15464.1	2108.6
		homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	159767	Squared		122475	37292

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.