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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 19268 in total

Value Type  : Measured

Rank	green	description	Network Comparison Type	network_comparison	Interaction Map	Filtered	red
1	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	36400000	High confidence	0	364
					Low confidence
	543.5	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		4.4149		1	2399.5
	2394.5	rad50-interacting protein 1. [refseq;acc:nm_021930]		5.31521	High confidence		450.5
	6410	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	6325		0	85
					Low confidence
	32028.5	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]		8870.5		1	40899
	33356.5	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	High confidence		41482.5
2	89	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	8900000	Low confidence	0	0.00001
	174	cab2. [refseq;acc:nm_033419]		17400000	High confidence
	543.5	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		4.4149	Low confidence	1	2399.5
	2394.5	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		5.31521	High confidence		450.5
	6410	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	6325		0	85
	19621.3	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		4196.8	Low confidence		23818.1
	28492	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		7307		1	21185
	33356.5	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		8126	High confidence		41482.5
3	89	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	8900000	Low confidence	0	0.00001
	109	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		10900000	High confidence
	543.5	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		4.4149	Low confidence	1	2399.5
	698.5	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		3.71868	High confidence		2597.5
	7500.75	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Subtracted	2393.82	Low confidence	0	5106.93
	19621.3	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		4196.8	High confidence		23818.1
	28492	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		7307	Low confidence	1	21185
	33356.5	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		8126	High confidence		41482.5
4	89	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	8900000	Low confidence	0	0.00001
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]			High confidence
	543.5	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]		4.4149	Low confidence	1	2399.5
	698.5	hbs1-like. [refseq;acc:nm_006620]		3.71868	High confidence		2597.5
	4356	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Subtracted	2274	Low confidence	0	2082
	21730	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]		3026	High confidence		18704
	33356.5	cytohesin 4. [swissprot;acc:q9uia0]		8126		1	41482.5
	43509.4	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]		7035.1	Low confidence		36474.3
5	17.5166	jumonji protein. [swissprot;acc:q92833]	Divided	1751660		0	0.00001
	89	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		8900000	High confidence
	339.5	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		3.39764		1	1153.5
	2113.5	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		2.86965	Low confidence		736.5
	2740.13	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	2254.84		0	485.286
	24446.3	histone h4. [swissprot;acc:p02304]		2673.2	High confidence		21773.1
	33356.5	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		8126		1	41482.5
	43503.3	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		7034	Low confidence		36469.3
6	0.00001	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Divided	1300000		0	13
	89	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		8900000	High confidence		0.00001
	339.5	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		3.39764		1	1153.5
	2113.5	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]		2.86965	Low confidence		736.5
	8836.85	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	1244.48		0	7592.37
	15605.1			2430.4	High confidence		13174.7
	36927.5	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		7563		1	44490.5
	43368.8	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		7008.5	Low confidence		36360.3
7	0.00001	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Divided	231962		0	2.31962
	43	sedlin. [swissprot;acc:o14582]		4300000	High confidence		0.00001

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.