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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

Rank	Network Comparison Type	Value Type	description	green	red	network_comparison	Filtered
1	Divided	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	364	36400000	0
			rad50-interacting protein 1. [refseq;acc:nm_021930]	2394.5	450.5	5.31521	1
		Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	4294	3.70633	0
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	10	2.4	1
		Squared	cab2. [refseq;acc:nm_033419]	7.16592	0.00001	716592	0
			rad50-interacting protein 1. [refseq;acc:nm_021930]	1357.07	48.0356	28.2513	1
		Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	19.0788	1907880	0
			rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	21.225	2.30547	1
	Subtracted	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	85	6325	0
			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]	33356.5	41482.5	8126	1
		Ranked	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	215	107
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	8906	12977	0
		Squared	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	232467	72283
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	322755	468498	145743	1
		Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	9.20014	50.8706	0
			rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	21.225	27.7086	1
2	Divided	Measured	cab2. [refseq;acc:nm_033419]	174	0.00001	17400000	0
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2394.5	450.5	5.31521	1
		Ranked	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]	28	15	1.86667
			mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	5865	2.55362	0
		Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	5.61325	561325
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1357.07	48.0356	28.2513	1
		Rooted	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	12.4097	1240970	0
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336	21.225	2.30547	1
	Subtracted	Measured	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	33356.5	41482.5	8126
			lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	85	6325	0
		Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	4294	11621
			hbs1-like. [refseq;acc:nm_006620]	322	215	107	1
		Squared	histone h4. [swissprot;acc:p02304]	345123	273623	71500	0
			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]	263351	407289	143938	1
		Rooted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	60.0707	9.20014	50.8706	0
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336	21.225	27.7086	1
3	Divided	Measured	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	698.5	2597.5	3.71868
			pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	0.00001	10900000	0
		Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	15	1.86667	1
			nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	4475.84	2.47638	0
		Squared	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	115.48	1596.92	13.8285	1
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	5.61325	561325	0
		Rooted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	26.4292	50.9657	1.92839	1
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	12.4097	1240970	0
	Subtracted	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	33356.5	41482.5	8126	1
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	23818.1	4196.8	0
		Ranked	cab2. [refseq;acc:nm_033419]	10950	21866	10916
			rad50-interacting protein 1. [refseq;acc:nm_021930]	232	337	105	1
		Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	170628	135280	35348	0
			cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	263351	407289	143938	1
		Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	6.85565	36.9188	30.0631	0
			homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	26.4292	50.9657	24.5365	1
4	Divided	Measured	hbs1-like. [refseq;acc:nm_006620]	698.5	2597.5	3.71868
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	0.00001	8900000	0

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.