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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Value Type  : Measured

Rank	Interaction Map	Network Comparison Type	description	Filtered	green	red	network_comparison
1	High confidence	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	0.00001	364	36400000
			rad50-interacting protein 1. [refseq;acc:nm_021930]	1	2394.5	450.5	5.31521
		Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	6410	85	6325
			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]	1	33356.5	41482.5	8126
	Low confidence	Divided	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		543.5	2399.5	4.4149
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	0.00001	364	36400000
		Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		6410	85	6325
			carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	1	32028.5	40899	8870.5
2	High confidence	Divided	cab2. [refseq;acc:nm_033419]	0	174	0.00001	17400000
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	2394.5	450.5	5.31521
		Subtracted	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		33356.5	41482.5	8126
			lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	6410	85	6325
	Low confidence	Divided	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	543.5	2399.5	4.4149
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	89	0.00001	8900000
		Subtracted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1	28492	21185	7307
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0	19621.3	23818.1	4196.8
3	High confidence	Divided	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	698.5	2597.5	3.71868
			pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	109	0.00001	10900000
		Subtracted	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	1	33356.5	41482.5	8126
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0	19621.3	23818.1	4196.8
	Low confidence	Divided	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	543.5	2399.5	4.4149
			homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	89	0.00001	8900000
		Subtracted	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1	28492	21185	7307
			nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	0	7500.75	5106.93	2393.82
4	High confidence	Divided	hbs1-like. [refseq;acc:nm_006620]	1	698.5	2597.5	3.71868
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	89	0.00001	8900000
		Subtracted	cytohesin 4. [swissprot;acc:q9uia0]	1	33356.5	41482.5	8126
			small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	0	21730	18704	3026
	Low confidence	Divided	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		89	0.00001	8900000
			lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	1	543.5	2399.5	4.4149
		Subtracted	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	0	4356	2082	2274
			bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	1	43509.4	36474.3	7035.1
5	High confidence	Divided	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	89	0.00001	8900000
			junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1	339.5	1153.5	3.39764
		Subtracted	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		33356.5	41482.5	8126
			histone h4. [swissprot;acc:p02304]	0	24446.3	21773.1	2673.2
	Low confidence	Divided	jumonji protein. [swissprot;acc:q92833]		17.5166	0.00001	1751660
			oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	1	2113.5	736.5	2.86965
		Subtracted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	2740.13	485.286	2254.84
			vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	1	43503.3	36469.3	7034
6	High confidence	Divided	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	89	0.00001	8900000
			junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1	339.5	1153.5	3.39764
		Subtracted	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		36927.5	44490.5	7563
			similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	0	15605.1	13174.7	2430.4
	Low confidence	Divided	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		0.00001	13	1300000
			oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	1	2113.5	736.5	2.86965
		Subtracted	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		43368.8	36360.3	7008.5
			similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	0	8836.85	7592.37	1244.48
7	High confidence	Divided	sedlin. [swissprot;acc:o14582]		43	0.00001	4300000
			sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	1	339.5	1153.5	3.39764

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.