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

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Showing element 1 to 50 of 19268 in total

Value Type  : Measured

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