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

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Showing element 1 to 50 of 19268 in total

Value Type  : Measured

Rank	green	network_comparison	description	Network Comparison Type	Interaction Map	Filtered	red
1	0.00001	36400000	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	High confidence	0	364
					Low confidence
	543.5	4.4149	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]			1	2399.5
	2394.5	5.31521	rad50-interacting protein 1. [refseq;acc:nm_021930]		High confidence		450.5
	6410	6325	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted		0	85
					Low confidence
	32028.5	8870.5	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]			1	40899
	33356.5	8126	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		41482.5
2	89	8900000	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	Low confidence	0	0.00001
	174	17400000	cab2. [refseq;acc:nm_033419]		High confidence
	543.5	4.4149	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		Low confidence	1	2399.5
	2394.5	5.31521	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		High confidence		450.5
	6410	6325	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted		0	85
	19621.3	4196.8	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Low confidence		23818.1
	28492	7307	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]			1	21185
	33356.5	8126	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		High confidence		41482.5
3	89	8900000	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	Low confidence	0	0.00001
	109	10900000	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		High confidence
	543.5	4.4149	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		Low confidence	1	2399.5
	698.5	3.71868	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		High confidence		2597.5
	7500.75	2393.82	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Subtracted	Low confidence	0	5106.93
	19621.3	4196.8	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		High confidence		23818.1
	28492	7307	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		Low confidence	1	21185
	33356.5	8126	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		High confidence		41482.5
4	89	8900000	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	Low confidence	0	0.00001
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		High confidence
	543.5	4.4149	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]		Low confidence	1	2399.5
	698.5	3.71868	hbs1-like. [refseq;acc:nm_006620]		High confidence		2597.5
	4356	2274	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Subtracted	Low confidence	0	2082
	21730	3026	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]		High confidence		18704
	33356.5	8126	cytohesin 4. [swissprot;acc:q9uia0]			1	41482.5
	43509.4	7035.1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]		Low confidence		36474.3
5	17.5166	1751660	jumonji protein. [swissprot;acc:q92833]	Divided		0	0.00001
	89	8900000	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		High confidence
	339.5	3.39764	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]			1	1153.5
	2113.5	2.86965	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		Low confidence		736.5
	2740.13	2254.84	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted		0	485.286
	24446.3	2673.2	histone h4. [swissprot;acc:p02304]		High confidence		21773.1
	33356.5	8126	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]			1	41482.5
	43503.3	7034	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		Low confidence		36469.3
6	0.00001	1300000	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Divided		0	13
	89	8900000	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		High confidence		0.00001
	339.5	3.39764	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]			1	1153.5
	2113.5	2.86965	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]		Low confidence		736.5
	8836.85	1244.48	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted		0	7592.37
	15605.1	2430.4			High confidence		13174.7
	36927.5	7563	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]			1	44490.5
	43368.8	7008.5	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Low confidence		36360.3
7	0.00001	231962	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Divided		0	2.31962
	43	4300000	sedlin. [swissprot;acc:o14582]		High confidence		0.00001

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.