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	network_comparison	red	Network Comparison Type	green	Filtered

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Showing element 1 to 50 of 19268 in total

Value Type  : Measured

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

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.