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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	Value Type	Filtered	description	Network Comparison Type	Interaction Map	green	red	network_comparison
1	Measured	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	High confidence	6410	85	6325
					Low confidence
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	High confidence	0.00001	364	36400000
					Low confidence
		1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Subtracted		32028.5	40899	8870.5
			lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided		543.5	2399.5	4.4149
			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	High confidence	33356.5	41482.5	8126
			rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided		2394.5	450.5	5.31521
	Ranked	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]			15915	4294	3.70633
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted		21883	8906	12977
					Low confidence
			mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided		14977	5865	2.55362
		1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]			32	16	2
			homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Subtracted	High confidence	322	215	107
			lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		Low confidence	330	223
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	High confidence	24	10	2.4
	Squared	0	cab2. [refseq;acc:nm_033419]			7.16592	0.00001	716592
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Low confidence	1.87479		187479
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	High confidence	160184	232467	72283
					Low confidence
		1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]			242799	395912	153113
			lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided		69.9153	1362.75	19.4914
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Subtracted	High confidence	322755	468498	145743
			rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided		1357.07	48.0356	28.2513
	Rooted	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted		60.0707	9.20014	50.8706
					Low confidence
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	High confidence	0.00001	19.0788	1907880
					Low confidence
		1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]			23.3131	48.9847	2.10117
				Subtracted				25.6716
			rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	High confidence	48.9336	21.225	2.30547
				Subtracted				27.7086
2	Measured	0	cab2. [refseq;acc:nm_033419]	Divided		174	0.00001	17400000
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Low confidence	89		8900000
			lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	High confidence	6410	85	6325
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Low confidence	19621.3	23818.1	4196.8
		1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]			28492	21185	7307
			cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Divided		543.5	2399.5	4.4149
			cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Subtracted	High confidence	33356.5	41482.5	8126
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided		2394.5	450.5	5.31521
	Ranked	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted		15915	4294	11621
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	Low confidence	21883	8906	2.45711
			mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		High confidence	14977	5865	2.55362
			neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Subtracted	Low confidence	20617	9607	11010
		1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]			330	223	107
			hbs1-like. [refseq;acc:nm_006620]		High confidence	322	215
			lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided	Low confidence	330	223	1.47982
			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]		High confidence	28	15	1.86667
	Squared	0	histone h4. [swissprot;acc:p02304]	Subtracted		345123	273623	71500
			homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	Low confidence	1.87479	0.00001	187479

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.