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

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Showing element 1 to 50 of 77072 in total

Network Comparison Type  : Divided
Value Type  : Measured

Rank	green	Interaction Map	description	network_comparison	red	Filtered
1	0.00001	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	36400000	364	0
		Low confidence
	543.5		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	4.4149	2399.5	1
	2394.5	High confidence	rad50-interacting protein 1. [refseq;acc:nm_021930]	5.31521	450.5
2	89	Low confidence	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	8900000	0.00001	0
	174	High confidence	cab2. [refseq;acc:nm_033419]	17400000
	543.5	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	4.4149	2399.5	1
	2394.5	High confidence	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	5.31521	450.5
3	89	Low confidence	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	8900000	0.00001	0
	109	High confidence	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	10900000
	543.5	Low confidence	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	4.4149	2399.5	1
	698.5	High confidence	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	3.71868	2597.5
4	89		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	8900000	0.00001	0
		Low confidence	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
	543.5		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	4.4149	2399.5	1
	698.5	High confidence	hbs1-like. [refseq;acc:nm_006620]	3.71868	2597.5
5	17.5166	Low confidence	jumonji protein. [swissprot;acc:q92833]	1751660	0.00001	0
	89	High confidence	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	8900000
	339.5		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	3.39764	1153.5	1
	2113.5	Low confidence	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	2.86965	736.5
6	0.00001		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	1300000	13	0
	89	High confidence	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	8900000	0.00001
	339.5		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	3.39764	1153.5	1
	2113.5	Low confidence	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	2.86965	736.5
7	0.00001		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	231962	2.31962	0
	43	High confidence	sedlin. [swissprot;acc:o14582]	4300000	0.00001
	339.5		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]	3.39764	1153.5	1
	2113.5	Low confidence	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	2.86965	736.5
8	43	High confidence	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	4300000	0.00001	0
	339.5		db83 protein. [swissprot;acc:p57088]	3.39764	1153.5	1
	5058.5	Low confidence	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	1.54317	3278
	6410		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	75.4118	85	0
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
	1281.5	High confidence	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	3.21581	398.5	1
	5058.5	Low confidence	n33 protein. [swissprot;acc:q13454]	1.54317	3278
	6410	High confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	75.4118	85	0
10	5.56738	Low confidence	serpin b12. [swissprot;acc:q96p63]	35.8425	199.549
	1281.5	High confidence	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	3.21581	398.5	1
	5058.5	Low confidence	implantation-associated protein. [refseq;acc:nm_032121]	1.54317	3278
	6410	High confidence	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	75.4118	85	0
11	5.56738		serpin b12. [swissprot;acc:q96p63]	35.8425	199.549
	5.71669	Low confidence	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	199.249
	1281.5	High confidence	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	3.21581	398.5	1
	2950.5	Low confidence	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	1.53861	1917.64
12	5.71669	High confidence	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	199.249	0
	58	Low confidence	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14.8103	859
	1281.5	High confidence	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	3.21581	398.5	1
	2954.24	Low confidence	gbp protein isoform a. [refseq;acc:nm_017870]	1.5371	1921.96
13	47	High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	29	1363	0
	115.385	Low confidence	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	8.11997

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.