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

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

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.