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

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Showing element 1 to 50 of 38536 in total

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

Rank	Interaction Map	description	red	green	network_comparison
1	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0.00001	36400000
	Low confidence
2	High confidence	cab2. [refseq;acc:nm_033419]	0.00001	174	17400000
	Low confidence	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		89	8900000
3	High confidence	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		109	10900000
	Low confidence	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		89	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	jumonji protein. [swissprot;acc:q92833]		17.5166	1751660
6	High confidence	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		89	8900000
	Low confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	13	0.00001	1300000
7	High confidence	sedlin. [swissprot;acc:o14582]	0.00001	43	4300000
	Low confidence	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	2.31962	0.00001	231962
8	High confidence	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0.00001	43	4300000
	Low confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	6410	75.4118
9	High confidence
	Low confidence	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	383.762	10.6048	36.1876
10	High confidence	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	85	6410	75.4118
	Low confidence	serpin b12. [swissprot;acc:q96p63]	199.549	5.56738	35.8425
11	High confidence
	Low confidence	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	199.249	5.71669	34.8539
12	High confidence
	Low confidence	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	58	14.8103
13	High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	1363	47	29
	Low confidence	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	115.385	14.21
14	High confidence	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	130.512	6.50325	20.0687
	Low confidence	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	59	5900000
15	High confidence	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	156	15.6
	Low confidence	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	485.286	2740.13	5.64642
16	High confidence	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	1	15	15
	Low confidence	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	125	704.5	5.636
17	High confidence	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	58	14.8103
	Low confidence	ptd016 protein. [refseq;acc:nm_016125]	30	158	5.26667
18	High confidence	60s ribosomal protein l37a. [swissprot;acc:p12751]	305.45	26.1599	11.6763
	Low confidence	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	99	19	5.21053
19	High confidence	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	26.1599	11.6763
	Low 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]	153	662	4.3268
20	High confidence	ero1-like. [refseq;acc:nm_014584]	82	0.00001	8200000
	Low confidence	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	570	139	4.10072
21	High confidence	syntaxin 10 (syn10). [swissprot;acc:o60499]	118.878	17.6611	6.73106
	Low confidence	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	434.911	3.90833
22	High confidence	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60	0.00001	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	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	59	5900000
	Low confidence	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	37	0.00001	3700000
24	High confidence	ptd016 protein. [refseq;acc:nm_016125]	30	158	5.26667
	Low confidence	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	154	493	3.2013
25	High confidence	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	148	773	5.22297
	Low confidence	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	12.6208	39.8063	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.