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

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Showing element 1 to 50 of 3730 in total

Value Type  : Measured
Interaction Map  : High confidence
Network Comparison Type  : Divided

Rank	description	red	network_comparison	Filtered	green
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	36400000	0	0.00001
	rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	5.31521	1	2394.5
2	cab2. [refseq;acc:nm_033419]	0.00001	17400000	0	174
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	5.31521	1	2394.5
3	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	3.71868		698.5
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0.00001	10900000	0	109
4	hbs1-like. [refseq;acc:nm_006620]	2597.5	3.71868	1	698.5
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	8900000	0	89
5	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1153.5	3.39764	1	339.5
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0.00001	8900000	0	89
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1153.5	3.39764	1	339.5
7	sedlin. [swissprot;acc:o14582]	0.00001	4300000	0	43
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	1153.5	3.39764	1	339.5
8	db83 protein. [swissprot;acc:p57088]
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0.00001	4300000	0	43
9	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	75.4118		6410
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	398.5	3.21581	1	1281.5
10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	85	75.4118	0	6410
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	398.5	3.21581	1	1281.5
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
	serpin b12. [swissprot;acc:q96p63]	199.549	35.8425	0	5.56738
12	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	398.5	3.21581	1	1281.5
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	199.249	34.8539	0	5.71669
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	1363	29		47
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	398.5	3.21581	1	1281.5
14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	130.512	20.0687	0	6.50325
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	398.5	3.21581	1	1281.5
15	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	0	156
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	2671	3.06659	1	871
16	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	1	15	0	15
	protein x 0004. [refseq;acc:nm_016301]	2671	3.06659	1	871
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	460	2.96739		1365
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	14.8103	0	58
18	60s ribosomal protein l37a. [swissprot;acc:p12751]	305.45	11.6763		26.1599
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	677.5	2.75351	1	1865.5
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]	305.45	11.6763	0	26.1599
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	677.5	2.75351	1	1865.5
20	ero1-like. [refseq;acc:nm_014584]	82	8200000	0	0.00001
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	677.5	2.75351	1	1865.5
21	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
	syntaxin 10 (syn10). [swissprot;acc:o60499]	118.878	6.73106	0	17.6611
22	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	677.5	2.75351	1	1865.5
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60	6000000	0	0.00001
23	gbp protein isoform a. [refseq;acc:nm_017870]	699.76	2.7072	1	1894.39
	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	0	59
24	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	950.561	2.21818	1	2108.52
	ptd016 protein. [refseq;acc:nm_016125]	30	5.26667	0	158
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1833.01	2.0534	1	892.67
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	148	5.22297	0	773

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.