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

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided

Rank	Interaction Map	green	description	red	network_comparison
1	High confidence	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	36400000
	Low confidence
2	High confidence	174	cab2. [refseq;acc:nm_033419]	0.00001	17400000
	Low confidence	89	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		8900000
3	High confidence	109	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		10900000
	Low confidence	89	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		8900000
4	High confidence		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]
	Low confidence		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
5	High confidence		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	Low confidence	17.5166	jumonji protein. [swissprot;acc:q92833]		1751660
6	High confidence	89	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		8900000
	Low confidence	0.00001	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	13	1300000
7	High confidence	43	sedlin. [swissprot;acc:o14582]	0.00001	4300000
	Low confidence	0.00001	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	2.31962	231962
8	High confidence	43	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0.00001	4300000
	Low confidence	6410	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	75.4118
9	High confidence
	Low confidence	10.6048	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	383.762	36.1876
10	High confidence	6410	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	85	75.4118
	Low confidence	5.56738	serpin b12. [swissprot;acc:q96p63]	199.549	35.8425
11	High confidence
	Low confidence	5.71669	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	199.249	34.8539
12	High confidence
	Low confidence	58	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	14.8103
13	High confidence	47	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	1363	29
	Low confidence	115.385	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]	8.11997	14.21
14	High confidence	6.50325	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	130.512	20.0687
	Low confidence	59	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	0.00001	5900000
15	High confidence	156	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]	10	15.6
	Low confidence	2740.13	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	485.286	5.64642
16	High confidence	15	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	1	15
	Low confidence	704.5	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	125	5.636
17	High confidence	58	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	14.8103
	Low confidence	158	ptd016 protein. [refseq;acc:nm_016125]	30	5.26667
18	High confidence	26.1599	60s ribosomal protein l37a. [swissprot;acc:p12751]	305.45	11.6763
	Low confidence	19	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	99	5.21053
19	High confidence	26.1599	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]	305.45	11.6763
	Low confidence	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]	153	4.3268
20	High confidence	0.00001	ero1-like. [refseq;acc:nm_014584]	82	8200000
	Low confidence	139	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	570	4.10072
21	High confidence	17.6611	syntaxin 10 (syn10). [swissprot;acc:o60499]	118.878	6.73106
	Low confidence	434.911	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	111.278	3.90833
22	High confidence	0.00001	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60	6000000
	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]	37	3700000
23	High confidence	59	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	0.00001	5900000
	Low confidence	0.00001	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	37	3700000
24	High confidence	158	ptd016 protein. [refseq;acc:nm_016125]	30	5.26667
	Low confidence	493	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	154	3.2013
25	High confidence	773	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	148	5.22297
	Low confidence	39.8063	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	12.6208	3.15402

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.