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

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Showing element 1 to 50 of 77072 in total

Filtered  : 0
Value Type  : Measured

network_comparison	green	Interaction Map	Network Comparison Type	red	Rank	description
0	0	High confidence	Subtracted	0	494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
					495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
					496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
					497	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
					498	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
					499	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
					500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
					501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
					502	brca1 associated protein. [refseq;acc:nm_006768]
		Low confidence			837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
					838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
					839	cobw-like protein. [refseq;acc:nm_018491]
					840	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
					841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
					842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
					843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
0.08	1589.95			1589.87	836	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]
0.15	1573.69			1573.54	835	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]
0.4	2710.41			2710.81	834	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]
0.562	249.857	High confidence		250.419	492	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]
					493	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
0.81	1242.41	Low confidence		1243.22	833	hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367]
1	0.00001	High confidence	Divided	0.00001	494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
					495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
					496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
					497	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
					498	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
					499	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
					500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
					501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
					502	brca1 associated protein. [refseq;acc:nm_006768]
		Low confidence			837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
					838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
					839	cobw-like protein. [refseq;acc:nm_018491]
					840	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
					841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
					842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
					843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
1.00005	1589.95			1589.87	836	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]
1.0001	1573.69			1573.54	835	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]
1.00015	2710.41			2710.81	834	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]
1.0002	9357.07			9355.21	833	ganglioside induced differentiation associated protein 2; likely ortholog of mouse ganglioside-induced differentiation-associated-protein 2. [refseq;acc:nm_017686]
1.00033	3507.42			3506.27	832	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]
1.00059	2411.78	High confidence		2410.35	493	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]
1.00065	1242.41	Low confidence		1243.22	831	hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367]
1.00074	3462.18			3464.75	830	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]
1.00086	1465.37			1464.11	829	alpha-nac protein. [sptrembl;acc:q9h009]
1.00124	1464.85			1463.03	828	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]
1.0013	1673.2			1675.38	827	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]
1.00138	14901.7			14922.2	826	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]

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.