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	Gene	Rank	green	description	Network Comparison Type	network_comparison	Interaction Map	red

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Showing element 1 to 50 of 38536 in total

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

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