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	description	Interaction Map	red	green	Network Comparison Type	Gene	Rank

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Showing element 1 to 50 of 77072 in total

Filtered  : 0
Value Type  : Measured

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

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.