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	Value Type	Rank	Gene	Interaction Map	description	red	green	Filtered	network_comparison

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Showing element 1 to 50 of 77072 in total

Network Comparison Type  : Divided
Value Type  : Measured

Rank	Interaction Map	description	red	green	Filtered	network_comparison
1	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0.00001	0	36400000
		rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	2394.5	1	5.31521
	Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	2399.5	543.5		4.4149
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0.00001	0	36400000
2	High confidence	cab2. [refseq;acc:nm_033419]	0.00001	174		17400000
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	2394.5	1	5.31521
	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	2399.5	543.5		4.4149
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	89	0	8900000
3	High confidence	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	698.5	1	3.71868
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0.00001	109	0	10900000
	Low confidence	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	2399.5	543.5	1	4.4149
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	89	0	8900000
4	High confidence	hbs1-like. [refseq;acc:nm_006620]	2597.5	698.5	1	3.71868
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	89	0	8900000
	Low confidence	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	2399.5	543.5	1	4.4149
5	High confidence	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	89	0	8900000
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1153.5	339.5	1	3.39764
	Low confidence	jumonji protein. [swissprot;acc:q92833]	0.00001	17.5166	0	1751660
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	736.5	2113.5	1	2.86965
6	High confidence	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0.00001	89	0	8900000
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1153.5	339.5	1	3.39764
	Low confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	13	0.00001	0	1300000
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	736.5	2113.5	1	2.86965
7	High confidence	sedlin. [swissprot;acc:o14582]	0.00001	43	0	4300000
		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	339.5	1	3.39764
	Low confidence	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	736.5	2113.5		2.86965
		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	2.31962	0.00001	0	231962
8	High confidence	db83 protein. [swissprot;acc:p57088]	1153.5	339.5	1	3.39764
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0.00001	43	0	4300000
	Low confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	6410		75.4118
		phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	3278	5058.5	1	1.54317
9	High confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	6410	0	75.4118
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	398.5	1281.5	1	3.21581
	Low confidence	n33 protein. [swissprot;acc:q13454]	3278	5058.5		1.54317
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	383.762	10.6048	0	36.1876
10	High confidence	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	85	6410		75.4118
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	398.5	1281.5	1	3.21581
	Low confidence	implantation-associated protein. [refseq;acc:nm_032121]	3278	5058.5		1.54317
		serpin b12. [swissprot;acc:q96p63]	199.549	5.56738	0	35.8425
11	High confidence	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	398.5	1281.5	1	3.21581
		serpin b12. [swissprot;acc:q96p63]	199.549	5.56738	0	35.8425
	Low confidence	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	199.249	5.71669		34.8539
		thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	1917.64	2950.5	1	1.53861
12	High confidence	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	398.5	1281.5		3.21581
		hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	199.249	5.71669	0	34.8539
	Low confidence	gbp protein isoform a. [refseq;acc:nm_017870]	1921.96	2954.24	1	1.5371
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	859	58	0	14.8103
13	High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	1363	47		29
		cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	398.5	1281.5	1	3.21581

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.