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 551 to 600 of 19268 in total

Value Type  : Ranked

Rank	description	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison
69	testis-specific protein tex28. [swissprot;acc:o15482]	Divided	Low confidence	1	259.517	235.017	1.10425
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]			0	15870.7	12610.3	1.25855
70	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]			1	259.517	235.017	1.10425
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]		High confidence		267.142	336.074	1.25804
	latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302]		Low confidence	0	9856	12392	1.25731
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Subtracted	High confidence		8082.33	5266.67	2815.66
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]		Low confidence	1	225.545	244.933	19.388
	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	Divided	High confidence	0	13975.7	10593.2	1.31931
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Subtracted		1	188.688	242.742	54.054
	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]		Low confidence	0	12242.7	9346.75	2895.95
71	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]		High confidence		13841.2	11127.5	2713.7
	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]	Divided	Low confidence	1	230.944	209.149	1.10421
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]		High confidence		267.144	336.073	1.25802
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Subtracted			265.686	319.651	53.965
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]		Low confidence	0	8082.33	5266.67	2815.66
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Divided	High confidence		4338.65	5700.79	1.31395
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]		Low confidence		11448.7	9117	1.25575
	transcription factor jun-d. [swissprot;acc:p17535]	Subtracted		1	202.709	183.361	19.348
72	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]			0	10172.1	12943.5	2771.4
	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Divided			17449	21866	1.25314
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]		High confidence	1	267.144	336.073	1.25802
	metaxin 1. [swissprot;acc:q13505]	Subtracted		0	13761.3	16422.1	2660.8
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]			1	265.639	319.546	53.907
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Divided		0	4119	5397	1.31027
	set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197]		Low confidence	1	230.944	209.149	1.10421
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Subtracted			227.623	208.281	19.342
73	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Divided		0	17449	21866	1.25314
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Subtracted			9282.29	6526.57	2755.72
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	High confidence	1	288	362	1.25694
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Subtracted			265.632	319.531	53.899
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]			0	9465.55	12106.5	2640.95
	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	Divided			4119	5397	1.31027
	set and mynd domain containing protein 1. [sptrembl;acc:q8nb12]		Low confidence	1	230.944	209.149	1.10421
	transcription factor jun-b. [swissprot;acc:p17275]	Subtracted			202.728	183.388	19.34
74	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Divided	High confidence	0	6742.5	8759.5	1.29915
	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	Subtracted			14548.5	11915.2	2633.3
	jumonji protein. [swissprot;acc:q92833]		Low confidence		22296.2	19621	2675.2
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	High confidence	1	288	362	1.25694
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]		Low confidence	0	5900.08	7386.89	1.252
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Subtracted		1	225.428	244.701	19.273
	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]	Divided			195.817	215.516	1.1006
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	Subtracted	High confidence		189.07	242.453	53.383
75	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]			0	8158	5530.5	2627.5
	bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2]		Low confidence		14899.4	17562.2	2662.8
	nanos (fragment). [sptrembl;acc:q8wy41]	Divided	High confidence		8782	11350	1.29242
	nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323]		Low confidence	1	249.709	226.944	1.10031
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted			221.194	202.005	19.189
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Divided	High confidence		288	362	1.25694
	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]		Low confidence	0	9688.47	12104.2	1.24934
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Subtracted	High confidence	1	254.693	202.668	52.025

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.