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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

Rank	Value Type	Filtered	description	Network Comparison Type	red	green	network_comparison
1	Measured	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
	Ranked	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		4294	15915	3.70633
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted	8906	21883	12977
		1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		215	322	107
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	10	24	2.4
	Squared	0	cab2. [refseq;acc:nm_033419]		0.00001	7.16592	716592
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	232467	160184	72283
		1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		468498	322755	145743
			rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	48.0356	1357.07	28.2513
	Rooted	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	9.20014	60.0707	50.8706
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	19.0788	0.00001	1907880
		1	rad50-interacting protein 1. [refseq;acc:nm_021930]		21.225	48.9336	2.30547
				Subtracted			27.7086
2	Measured	0	cab2. [refseq;acc:nm_033419]	Divided	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
	Ranked	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted	4294	15915	11621
			mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	5865	14977	2.55362
		1	hbs1-like. [refseq;acc:nm_006620]	Subtracted	215	322	107
			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]	Divided	15	28	1.86667
	Squared	0	histone h4. [swissprot;acc:p02304]	Subtracted	273623	345123	71500
			nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	5.61325	0.00001	561325
		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	407289	263351	143938
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	48.0356	1357.07	28.2513
	Rooted	0	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	9.20014	60.0707	50.8706
			nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	12.4097	0.00001	1240970
		1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		21.225	48.9336	2.30547
				Subtracted			27.7086
3	Measured	0	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		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
	Ranked	0	cab2. [refseq;acc:nm_033419]	Subtracted	21866	10950	10916
			nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Divided	4475.84	11083.9	2.47638
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		15	28	1.86667
			rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted	337	232	105
	Squared	0	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]		135280	170628	35348
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	5.61325	0.00001	561325
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Subtracted	407289	263351	143938
			homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	1596.92	115.48	13.8285
	Rooted	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted	36.9188	6.85565	30.0631
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	12.4097	0.00001	1240970
		1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		50.9657	26.4292	1.92839
				Subtracted			24.5365
4	Measured	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

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.