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

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Showing element 1 to 50 of 77072 in total

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

Rank	description	Interaction Map	network_comparison	green	red
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	36400000	0.00001	364
		Low confidence
2	cab2. [refseq;acc:nm_033419]	High confidence	17400000	174	0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Low confidence	8900000	89
3	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence	10900000	109
4	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	8900000	89
	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]	Low confidence	1751660	17.5166
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	High confidence	8900000	89
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence	1300000	0.00001	13
7	sedlin. [swissprot;acc:o14582]	High confidence	4300000	43	0.00001
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Low confidence	231962	0.00001	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]	High confidence	4300000	43	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]	Low confidence	36.1876	10.6048	383.762
10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	High confidence	75.4118	6410	85
	serpin b12. [swissprot;acc:q96p63]	Low confidence	35.8425	5.56738	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]	High confidence	35.8425	5.56738	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]	Low confidence	14.8103	58	859
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	High confidence	29	47	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]	Low confidence	14.21	115.385	8.11997
14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	High confidence	20.0687	6.50325	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]	Low confidence	5900000	59	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]	High confidence	15.6	156	10
16	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	Low confidence	5.636	704.5	125
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	High confidence	15	15	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]	Low confidence	5.26667	158	30
18	60s ribosomal protein l37a. [swissprot;acc:p12751]	High confidence	11.6763	26.1599	305.45
	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	Low confidence	5.21053	19	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]	High confidence	11.6763	26.1599	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]	Low confidence	4.3268	662	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]	High confidence	8200000	0.00001	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]	Low confidence	3.90833	434.911	111.278
	syntaxin 10 (syn10). [swissprot;acc:o60499]	High confidence	6.73106	17.6611	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]	Low confidence	3700000	0.00001	37
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	High confidence	6000000		60
23	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Low confidence	3700000		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]	High confidence	5900000	59	0.00001
24	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	Low confidence	3.2013	493	154
	ptd016 protein. [refseq;acc:nm_016125]	High confidence	5.26667	158	30
25	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Low confidence	3.15402	39.8063	12.6208
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	High confidence	5.22297	773	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.