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	Gene	green	Rank	Interaction Map	description	network_comparison	Network Comparison Type	red

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Showing element 1 to 50 of 2158 in total

Filtered  : 0
Network Comparison Type  : Subtracted
red  : 0

Value Type	green	Rank	Interaction Map	description	network_comparison
Measured	0	494	High confidence	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	0
		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]
		837	Low confidence	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]
	17.5166	755		jumonji protein. [swissprot;acc:q92833]	17.5166
	18	428	High confidence	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	18
	43	376		sedlin. [swissprot;acc:o14582]	43
		377		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
	59	342		guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	59
		554	Low confidence
	89	289	High confidence	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89
		290		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
		291		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
		461	Low confidence	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]
		462		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
		463		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
	109	265	High confidence	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109
	174	185		cab2. [refseq;acc:nm_033419]	174
Ranked	0	501		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0
		502		brca1 associated protein. [refseq;acc:nm_006768]
		837	Low confidence	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]
		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]
Squared		494	High confidence	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]
		837	Low confidence	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]

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.