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

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Showing element 1 to 50 of 77072 in total

Value Type  : Measured

Rank	Filtered	description	Interaction Map	network_comparison	Network Comparison Type	red	green
1	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	High confidence	6325	Subtracted	85	6410
			Low confidence
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	36400000	Divided	364	0.00001
			Low confidence
	1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]		8870.5	Subtracted	40899	32028.5
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		4.4149	Divided	2399.5	543.5
		mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	High confidence	8126	Subtracted	41482.5	33356.5
		rad50-interacting protein 1. [refseq;acc:nm_021930]		5.31521	Divided	450.5	2394.5
2	0	cab2. [refseq;acc:nm_033419]		17400000		0.00001	174
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Low confidence	8900000			89
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	High confidence	6325	Subtracted	85	6410
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Low confidence	4196.8		23818.1	19621.3
	1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		7307		21185	28492
		cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		4.4149	Divided	2399.5	543.5
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	High confidence	8126	Subtracted	41482.5	33356.5
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		5.31521	Divided	450.5	2394.5
3	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Low confidence	8900000		0.00001	89
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	High confidence	4196.8	Subtracted	23818.1	19621.3
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Low confidence	2393.82		5106.93	7500.75
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	High confidence	10900000	Divided	0.00001	109
	1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Low confidence	4.4149		2399.5	543.5
		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	High confidence	8126	Subtracted	41482.5	33356.5
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		3.71868	Divided	2597.5	698.5
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Low confidence	7307	Subtracted	21185	28492
4	0	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]		2274		2082	4356
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		8900000	Divided	0.00001	89
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	High confidence
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]		3026	Subtracted	18704	21730
	1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Low confidence	7035.1		36474.3	43509.4
		cytohesin 4. [swissprot;acc:q9uia0]	High confidence	8126		41482.5	33356.5
		hbs1-like. [refseq;acc:nm_006620]		3.71868	Divided	2597.5	698.5
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	4.4149		2399.5	543.5
5	0	histone h4. [swissprot;acc:p02304]	High confidence	2673.2	Subtracted	21773.1	24446.3
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		8900000	Divided	0.00001	89
		jumonji protein. [swissprot;acc:q92833]	Low confidence	1751660			17.5166
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		2254.84	Subtracted	485.286	2740.13
	1	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	High confidence	8126		41482.5	33356.5
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		3.39764	Divided	1153.5	339.5
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Low confidence	2.86965		736.5	2113.5
		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		7034	Subtracted	36469.3	43503.3
6	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	High confidence	8900000	Divided	0.00001	89
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence	1300000		13	0.00001
		similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	High confidence	2430.4	Subtracted	13174.7	15605.1
			Low confidence	1244.48		7592.37	8836.85
	1	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	High confidence	3.39764	Divided	1153.5	339.5
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Low confidence	7008.5	Subtracted	36360.3	43368.8
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]		2.86965	Divided	736.5	2113.5
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	High confidence	7563	Subtracted	44490.5	36927.5
7	0	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Low confidence	1238.62		4660.09	5898.71
		sedlin. [swissprot;acc:o14582]	High confidence	4300000	Divided	0.00001	43

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.