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

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Showing element 1 to 50 of 38536 in total

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

Rank	description	network_comparison	green	Interaction Map	red
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	36400000	0.00001	High confidence	364
				Low confidence
2	cab2. [refseq;acc:nm_033419]	17400000	174	High confidence	0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	8900000	89	Low confidence
3	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	10900000	109	High confidence
4	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	8900000	89	Low confidence
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]			High confidence
5	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	jumonji protein. [swissprot;acc:q92833]	1751660	17.5166	Low confidence
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	8900000	89	High confidence
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	1300000	0.00001	Low confidence	13
7	sedlin. [swissprot;acc:o14582]	4300000	43	High confidence	0.00001
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	231962	0.00001	Low confidence	2.31962
8	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	75.4118	6410		85
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	4300000	43	High confidence	0.00001
9	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	75.4118	6410		85
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	36.1876	10.6048	Low confidence	383.762
10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	75.4118	6410	High confidence	85
	serpin b12. [swissprot;acc:q96p63]	35.8425	5.56738	Low confidence	199.549
11	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	5.71669		199.249
	serpin b12. [swissprot;acc:q96p63]	35.8425	5.56738	High confidence	199.549
12	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	5.71669		199.249
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14.8103	58	Low confidence	859
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	29	47	High confidence	1363
	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]	14.21	115.385	Low confidence	8.11997
14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	20.0687	6.50325	High confidence	130.512
	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]	5900000	59	Low confidence	0.00001
15	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	5.64642	2740.13		485.286
	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]	15.6	156	High confidence	10
16	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	5.636	704.5	Low confidence	125
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	15	15	High confidence	1
17	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14.8103	58		859
	ptd016 protein. [refseq;acc:nm_016125]	5.26667	158	Low confidence	30
18	60s ribosomal protein l37a. [swissprot;acc:p12751]	11.6763	26.1599	High confidence	305.45
	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	5.21053	19	Low confidence	99
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]	11.6763	26.1599	High confidence	305.45
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	4.3268	662	Low confidence	153
20	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	4.10072	139		570
	ero1-like. [refseq;acc:nm_014584]	8200000	0.00001	High confidence	82
21	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	3.90833	434.911	Low confidence	111.278
	syntaxin 10 (syn10). [swissprot;acc:o60499]	6.73106	17.6611	High confidence	118.878
22	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	3700000	0.00001	Low confidence	37
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	6000000		High confidence	60
23	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	3700000		Low confidence	37
	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]	5900000	59	High confidence	0.00001
24	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	3.2013	493	Low confidence	154
	ptd016 protein. [refseq;acc:nm_016125]	5.26667	158	High confidence	30
25	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	3.15402	39.8063	Low confidence	12.6208
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	5.22297	773	High confidence	148

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.