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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 19268 in total

Value Type  : Measured

Rank	Interaction Map	Filtered	description	Network Comparison Type	red	green	network_comparison
1	High confidence	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	85	6410	6325
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	364	0.00001	36400000
		1	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]	Subtracted	41482.5	33356.5	8126
			rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	450.5	2394.5	5.31521
	Low confidence	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	85	6410	6325
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	364	0.00001	36400000
		1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Subtracted	40899	32028.5	8870.5
			lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided	2399.5	543.5	4.4149
2	High confidence	0	cab2. [refseq;acc:nm_033419]		0.00001	174	17400000
			lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	85	6410	6325
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		41482.5	33356.5	8126
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	450.5	2394.5	5.31521
	Low confidence	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		0.00001	89	8900000
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	23818.1	19621.3	4196.8
		1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		21185	28492	7307
			cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Divided	2399.5	543.5	4.4149
3	High confidence	0	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	23818.1	19621.3	4196.8
			pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	0.00001	109	10900000
		1	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Subtracted	41482.5	33356.5	8126
			homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	2597.5	698.5	3.71868
	Low confidence	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		0.00001	89	8900000
			nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Subtracted	5106.93	7500.75	2393.82
		1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Divided	2399.5	543.5	4.4149
			mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted	21185	28492	7307
4	High confidence	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	0.00001	89	8900000
			small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Subtracted	18704	21730	3026
		1	cytohesin 4. [swissprot;acc:q9uia0]		41482.5	33356.5	8126
			hbs1-like. [refseq;acc:nm_006620]	Divided	2597.5	698.5	3.71868
	Low confidence	0	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Subtracted	2082	4356	2274
			homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	0.00001	89	8900000
		1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Subtracted	36474.3	43509.4	7035.1
			lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Divided	2399.5	543.5	4.4149
5	High confidence	0	histone h4. [swissprot;acc:p02304]	Subtracted	21773.1	24446.3	2673.2
			homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	0.00001	89	8900000
		1	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Subtracted	41482.5	33356.5	8126
			junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	1153.5	339.5	3.39764
	Low confidence	0	jumonji protein. [swissprot;acc:q92833]		0.00001	17.5166	1751660
			lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	485.286	2740.13	2254.84
		1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Divided	736.5	2113.5	2.86965
			vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Subtracted	36469.3	43503.3	7034
6	High confidence	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	0.00001	89	8900000
			similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	13174.7	15605.1	2430.4
		1	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	1153.5	339.5	3.39764
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Subtracted	44490.5	36927.5	7563
	Low confidence	0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Divided	13	0.00001	1300000
			similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	7592.37	8836.85	1244.48
		1	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		36360.3	43368.8	7008.5
			oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Divided	736.5	2113.5	2.86965
7	High confidence	0	sedlin. [swissprot;acc:o14582]		0.00001	43	4300000
			zinc finger protein 277. [swissprot;acc:q9nrm2]	Subtracted	13174.7	15605.1	2430.4

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.