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

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Showing element 1 to 50 of 19268 in total

Value Type  : Measured

Rank	Interaction Map	Filtered	description	Network Comparison Type	green	red	network_comparison
1	High confidence	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	6410	85	6325
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	0.00001	364	36400000
		1	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]	Subtracted	33356.5	41482.5	8126
			rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	2394.5	450.5	5.31521
	Low confidence	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	6410	85	6325
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	0.00001	364	36400000
		1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Subtracted	32028.5	40899	8870.5
			lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided	543.5	2399.5	4.4149
2	High confidence	0	cab2. [refseq;acc:nm_033419]		174	0.00001	17400000
			lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	6410	85	6325
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		33356.5	41482.5	8126
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	2394.5	450.5	5.31521
	Low confidence	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		89	0.00001	8900000
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	19621.3	23818.1	4196.8
		1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		28492	21185	7307
			cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Divided	543.5	2399.5	4.4149
3	High confidence	0	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	19621.3	23818.1	4196.8
			pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	109	0.00001	10900000
		1	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Subtracted	33356.5	41482.5	8126
			homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	698.5	2597.5	3.71868
	Low confidence	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		89	0.00001	8900000
			nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Subtracted	7500.75	5106.93	2393.82
		1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Divided	543.5	2399.5	4.4149
			mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted	28492	21185	7307
4	High confidence	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	89	0.00001	8900000
			small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Subtracted	21730	18704	3026
		1	cytohesin 4. [swissprot;acc:q9uia0]		33356.5	41482.5	8126
			hbs1-like. [refseq;acc:nm_006620]	Divided	698.5	2597.5	3.71868
	Low confidence	0	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Subtracted	4356	2082	2274
			homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	89	0.00001	8900000
		1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Subtracted	43509.4	36474.3	7035.1
			lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Divided	543.5	2399.5	4.4149
5	High confidence	0	histone h4. [swissprot;acc:p02304]	Subtracted	24446.3	21773.1	2673.2
			homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	89	0.00001	8900000
		1	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Subtracted	33356.5	41482.5	8126
			junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	339.5	1153.5	3.39764
	Low confidence	0	jumonji protein. [swissprot;acc:q92833]		17.5166	0.00001	1751660
			lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	2740.13	485.286	2254.84
		1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Divided	2113.5	736.5	2.86965
			vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Subtracted	43503.3	36469.3	7034
6	High confidence	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	89	0.00001	8900000
			similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	15605.1	13174.7	2430.4
		1	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	339.5	1153.5	3.39764
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Subtracted	36927.5	44490.5	7563
	Low confidence	0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Divided	0.00001	13	1300000
			similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	8836.85	7592.37	1244.48
		1	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		43368.8	36360.3	7008.5
			oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Divided	2113.5	736.5	2.86965
7	High confidence	0	sedlin. [swissprot;acc:o14582]		43	0.00001	4300000
			zinc finger protein 277. [swissprot;acc:q9nrm2]	Subtracted	15605.1	13174.7	2430.4

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.