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

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Showing element 1 to 50 of 29840 in total

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

Rank	network_comparison	description	red	Filtered	green
1	5.31521	rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	1	2394.5
	36400000	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0	0.00001
2	5.31521	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	1	2394.5
	17400000	cab2. [refseq;acc:nm_033419]	0.00001	0	174
3	3.71868	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	1	698.5
	10900000	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0.00001	0	109
4	3.71868	hbs1-like. [refseq;acc:nm_006620]	2597.5	1	698.5
	8900000	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	0	89
5	3.39764	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1153.5	1	339.5
	8900000	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	0	89
6	3.39764	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1153.5	1	339.5
	8900000	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0.00001	0	89
7	3.39764	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	1	339.5
	4300000	sedlin. [swissprot;acc:o14582]	0.00001	0	43
8	3.39764	db83 protein. [swissprot;acc:p57088]	1153.5	1	339.5
	4300000	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0.00001	0	43
9	3.21581	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	398.5	1	1281.5
	75.4118	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	0	6410
10	3.21581	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	398.5	1	1281.5
	75.4118	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	85	0	6410
11	3.21581	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	398.5	1	1281.5
	35.8425	serpin b12. [swissprot;acc:q96p63]	199.549	0	5.56738
12	3.21581	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	398.5	1	1281.5
	34.8539	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	199.249	0	5.71669
13	3.21581	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	398.5	1	1281.5
	29	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	1363	0	47
14	3.21581	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	398.5	1	1281.5
	20.0687	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	130.512	0	6.50325
15	3.06659	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	2671	1	871
	15.6	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	0	156
16	3.06659	protein x 0004. [refseq;acc:nm_016301]	2671	1	871
	15	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	1	0	15
17	2.96739	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	460	1	1365
	14.8103	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	0	58
18	2.75351	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	677.5	1	1865.5
	11.6763	60s ribosomal protein l37a. [swissprot;acc:p12751]	305.45	0	26.1599
19	2.75351	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	677.5	1	1865.5
	11.6763	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	0	26.1599
20	2.75351	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	677.5	1	1865.5
	8200000	ero1-like. [refseq;acc:nm_014584]	82	0	0.00001
21	2.75351	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	677.5	1	1865.5
	6.73106	syntaxin 10 (syn10). [swissprot;acc:o60499]	118.878	0	17.6611
22	2.75351	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	1	1865.5
	6000000	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60	0	0.00001
23	2.7072	gbp protein isoform a. [refseq;acc:nm_017870]	699.76	1	1894.39
	5900000	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	0	59
24	2.21818	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	950.561	1	2108.52
	5.26667	ptd016 protein. [refseq;acc:nm_016125]	30	0	158
25	2.0534	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1833.01	1	892.67
	5.22297	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	148	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.