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	network_comparison	red

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

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.