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

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Showing element 1 to 50 of 14920 in total

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

Rank	Value Type	description	green	network_comparison	red
1	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	36400000	364
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	3.70633	4294
	Squared	cab2. [refseq;acc:nm_033419]	7.16592	716592	0.00001
	Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	1907880	19.0788
2	Measured	cab2. [refseq;acc:nm_033419]	174	17400000	0.00001
	Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	2.55362	5865
	Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	561325	5.61325
	Rooted			1240970	12.4097
3	Measured	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	10900000	0.00001
	Ranked	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	2.47638	4475.84
	Squared	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	561325	5.61325
	Rooted			1240970	12.4097
4	Measured	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	8900000	0.00001
	Ranked	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	2.45711	8906
	Squared	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	2.81207	281207	0.00001
	Rooted		10.4403	1044030
5	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	8900000
	Ranked	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7	2.17144	5510.5
	Squared	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	187479	0.00001
	Rooted		9.43398	943398
6	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	8900000
	Ranked	ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2	2.03897	7523
	Squared	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	187479	0.00001
	Rooted		9.43398	943398
7	Measured	sedlin. [swissprot;acc:o14582]	43	4300000
	Ranked	cab2. [refseq;acc:nm_033419]	10950	1.99689	21866
	Squared	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.87479	187479	0.00001
	Rooted		9.43398	943398
8	Measured	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	43	4300000
	Ranked	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	21888	1.89918	11525
	Squared	ero1-like. [refseq;acc:nm_014584]	0.00001	159148	1.59148
	Rooted			905539	9.05539
9	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	75.4118	85
	Ranked	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	21888	1.89918	11525
	Squared	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0.00001	85207.1	0.852071
	Rooted			774597	7.74597
10	Measured	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	75.4118	85
	Ranked	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	14178.1	1.88805	7509.39
	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	0.00001
	Rooted		7.68115	768115
11	Measured	serpin b12. [swissprot;acc:q96p63]	5.56738	35.8425	199.549
	Ranked	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	6248	1.86092	11627
	Squared	sedlin. [swissprot;acc:o14582]	0.437633	43763.3	0.00001
	Rooted		6.55744	655744
12	Measured	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669	34.8539	199.249
	Ranked	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	5208.84	1.81023	9429.18
	Squared	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0.437633	43763.3	0.00001
	Rooted		6.55744	655744
13	Measured	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	47	29	1363
	Ranked	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	9264.5	1.77804	5210.5

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.