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

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Showing element 1 to 50 of 29840 in total

Network Comparison Type  : Divided
red  : 0.00001
Interaction Map  : High confidence
Filtered  : 0

Rank	Value Type	description	green	network_comparison
1	Squared	cab2. [refseq;acc:nm_033419]	7.16592	716592
2	Measured		174	17400000
3		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	10900000
4		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	8900000
	Squared	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	2.81207	281207
	Rooted		10.4403	1044030
5	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	8900000
	Squared	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	187479
	Rooted		9.43398	943398
6	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	8900000
	Squared	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	187479
	Rooted		9.43398	943398
7	Measured	sedlin. [swissprot;acc:o14582]	43	4300000
	Squared	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.87479	187479
	Rooted		9.43398	943398
8	Measured	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	43	4300000
10	Squared	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]	0.823905	82390.5
	Rooted		7.68115	768115
11	Squared	sedlin. [swissprot;acc:o14582]	0.437633	43763.3
	Rooted		6.55744	655744
12	Squared	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0.437633	43763.3
	Rooted		6.55744	655744
14		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]	4.24264	424264
16	Squared		0.0766864	7668.64
23	Measured	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	5900000
64		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	1800000
93	Rooted	cab2. [refseq;acc:nm_033419]	13.1909	1319090
494	Measured	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	0.00001	1
	Squared
	Rooted
495	Measured	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
	Squared
	Rooted
496	Measured	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
	Squared
	Rooted
497	Measured	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
	Squared
	Rooted
498	Measured	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
	Squared
	Rooted
499	Measured	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
	Squared
	Rooted
500	Measured	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
	Squared
	Rooted
501	Measured	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
	Ranked	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]

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.