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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

Rank	Value Type	description	Network Comparison Type	Filtered	green	red	network_comparison
1	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	0	6410	85	6325
		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	41482.5	8126
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	0	0.00001	364	36400000
		rad50-interacting protein 1. [refseq;acc:nm_021930]		1	2394.5	450.5	5.31521
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		0	15915	4294	3.70633
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Subtracted	1	322	215	107
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		0	21883	8906	12977
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	1	24	10	2.4
	Squared	cab2. [refseq;acc:nm_033419]		0	7.16592	0.00001	716592
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted		160184	232467	72283
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		1	322755	468498	145743
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided		1357.07	48.0356	28.2513
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	0	60.0707	9.20014	50.8706
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided		0.00001	19.0788	1907880
		rad50-interacting protein 1. [refseq;acc:nm_021930]		1	48.9336	21.225	2.30547
			Subtracted				27.7086
2	Measured	cab2. [refseq;acc:nm_033419]	Divided	0	174	0.00001	17400000
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Subtracted	1	33356.5	41482.5	8126
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		0	6410	85	6325
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	1	2394.5	450.5	5.31521
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted	0	15915	4294	11621
		hbs1-like. [refseq;acc:nm_006620]		1	322	215	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		28	15	1.86667
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		0	14977	5865	2.55362
	Squared	histone h4. [swissprot;acc:p02304]	Subtracted		345123	273623	71500
		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	263351	407289	143938
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	0	0.00001	5.61325	561325
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		1	1357.07	48.0356	28.2513
	Rooted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	0	60.0707	9.20014	50.8706
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided		0.00001	12.4097	1240970
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		1	48.9336	21.225	2.30547
			Subtracted				27.7086
3	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]			33356.5	41482.5	8126
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided		698.5	2597.5	3.71868
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	0	19621.3	23818.1	4196.8
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided		109	0.00001	10900000
	Ranked	cab2. [refseq;acc:nm_033419]	Subtracted		10950	21866	10916
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Divided	1	28	15	1.86667
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		0	11083.9	4475.84	2.47638
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted	1	232	337	105
	Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]		0	170628	135280	35348
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		1	263351	407289	143938
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided		115.48	1596.92	13.8285
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		0	0.00001	5.61325	561325
	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted		6.85565	36.9188	30.0631
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	1	26.4292	50.9657	1.92839
			Subtracted				24.5365
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	0	0.00001	12.4097	1240970
4	Measured	cytohesin 4. [swissprot;acc:q9uia0]	Subtracted	1	33356.5	41482.5	8126
		hbs1-like. [refseq;acc:nm_006620]	Divided		698.5	2597.5	3.71868

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.