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

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Showing element 1651 to 1700 of 8289 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Interaction Map	red	green	network_comparison
826	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993]	High confidence	223.186	213.912	1.04335
	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	Low confidence	201.026	195.916	1.02608
827	loh1cr12. [refseq;acc:nm_058169]	High confidence	230.087	220.579	1.0431
	serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269]	Low confidence	207.116	201.851	1.02608
828	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073]		204.206	199.02	1.02606
	unr protein. [swissprot;acc:o75534]	High confidence	230.087	220.579	1.0431
829	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]		135.844	130.259	1.04288
	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914]	Low confidence	202.608	197.472	1.02601
830	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]		201.067	195.971	1.026
	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	High confidence	231.734	222.222	1.0428
831	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
	trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6]	Low confidence	204.064	198.895	1.02599
832	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	High confidence	231.734	222.222	1.0428
	gamma-aminobutyric acid type b receptor, subunit 2 precursor (gaba-b receptor 2) (gaba-b-r2) (gb2) (gababr2) (g protein-coupled receptor 51) (gpr 51) (hg20). [swissprot;acc:o75899]	Low confidence	204.064	198.895	1.02599
833	gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	High confidence	231.734	222.222	1.0428
834	60s ribosomal protein l8. [swissprot;acc:p25120]
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Low confidence	206.26	201.038	1.02598
835	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	High confidence	231.734	222.222	1.0428
	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177]	Low confidence	202.578	197.45	1.02597
836	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	High confidence	231.734	222.222	1.0428
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Low confidence	202.357	197.234	1.02597
837	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]		194.47	189.552	1.02595
	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	High confidence	231.734	222.222	1.0428
838	lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760]	Low confidence	194.47	189.552	1.02595
	rw1 protein (fragment). [swissprot;acc:q92545]	High confidence	231.734	222.222	1.0428
839	lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330]	Low confidence	194.47	189.552	1.02595
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	High confidence	177.776	170.499	1.04268
840	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]		198.781	190.66	1.04259
	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	Low confidence	201.924	196.817	1.02595
841	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]		206.243	201.027
	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]	High confidence	198.781	190.66	1.04259
842	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	Low confidence	206.244	201.028	1.02595
	jm1 protein. [refseq;acc:nm_014008]	High confidence	219.762	210.806	1.04248
843	lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260]	Low confidence	194.47	189.552	1.02595
	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102]	High confidence	218.521	227.796	1.04244
844	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]	Low confidence	194.659	189.74	1.02592
	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	High confidence	178.033	170.82	1.04223
845	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Low confidence	209.59	215.023	1.02592
	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	High confidence	228.599	219.399	1.04193
846	forkhead box protein o1a (forkhead in rhabdomyosarcoma). [swissprot;acc:q12778]	Low confidence	204.497	199.336	1.02589
	methyltransferase like 2. [refseq;acc:nm_018396]	High confidence	147.211	153.371	1.04184
847	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	Low confidence	203.643	198.505	1.02588
848	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	High confidence	147.211	153.371	1.04184
	monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021]	Low confidence	181.638	177.058	1.02587
849	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	High confidence	147.211	153.371	1.04184
	solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593]	Low confidence	181.639	177.059	1.02587
850	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	High confidence	107.842	112.329	1.04161
	ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441]	Low confidence	197.337	192.361	1.02587

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.