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

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Showing element 1 to 50 of 77072 in total

Value Type  : Measured

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

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.