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	Interaction Map	Filtered	red	green	network_comparison

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Showing element 5308 to 5357 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
664	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Measured	Subtracted	6231.31	6933.9	702.59
	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]		Divided	6374.65	7145.59	1.12094
	similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]	Ranked	Subtracted	214.256	202.141	12.115
	ubiquitin-like protein smt3a. [swissprot;acc:p55854]	Squared	Divided	23948	28164.1	1.17605
	vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4]		Subtracted	25911.5	30281.9	4370.4
665	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]	Ranked	Divided	229.072	216.576	1.0577
	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]		Subtracted	214.254	202.166	12.088
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Measured		4108.15	4808.93	700.78
	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]		Divided	6374.65	7145.59	1.12094
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Rooted	Subtracted	50.0513	45.4124	4.6389
	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]		Divided	51.6042	55.574	1.07693
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Squared		18960.3	22298	1.17604
	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281]		Subtracted	25911.8	30282.2	4370.4
666	down-regulated in metastasis. [refseq;acc:nm_014503]	Rooted	Divided	51.6042	55.574	1.07693
	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668]	Measured	Subtracted	6781.05	7480.15	699.1
	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]	Ranked		250.465	238.38	12.085
	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057]	Squared	Divided	29224	34362.1	1.17582
	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	Rooted	Subtracted	61.5558	66.1861	4.6303
	tbc1 domain family member 5. [swissprot;acc:q92609]	Measured	Divided	6374.65	7145.59	1.12094
	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]	Ranked		229.072	216.576	1.0577
	yeast sec31p homolog. [refseq;acc:nm_014933]	Squared	Subtracted	25911.7	30282.1	4370.4
667	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Measured		10075.5	9377.75	697.75
	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]	Ranked	Divided	229.072	216.576	1.0577
	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272]	Squared		29224	34362.1	1.17582
	t54 protein. [swissprot;acc:q92917]	Rooted	Subtracted	61.5558	66.1861	4.6303
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Ranked		250.465	238.38	12.085
	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]	Measured	Divided	6374.65	7145.59	1.12094
	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	Rooted		51.2483	47.5889	1.0769
	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348]	Squared	Subtracted	25911.5	30281.9	4370.4
668	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	Ranked	Divided	229.072	216.576	1.0577
	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	Rooted		95.4476	102.785	1.07687
	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]	Measured	Subtracted	10075.5	9377.75	697.75
	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	Ranked		244.495	232.419	12.076
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Squared	Divided	23969.3	28175.3	1.17547
	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	Rooted	Subtracted	50.0015	54.627	4.6255
	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543]	Squared		25911.7	30282.1	4370.4
	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]	Measured	Divided	6374.65	7145.59	1.12094
669	40s ribosomal protein s23. [swissprot;acc:p39028]	Rooted	Subtracted	49.8325	45.2077	4.6248
	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]	Measured		10075.5	9377.75	697.75
	ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]	Squared		25911.7	30282.1	4370.4
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Rooted	Divided	79.931	86.0693	1.07679
	numb-like protein (numb-r). [swissprot;acc:q9y6r0]	Measured		6374.65	7145.59	1.12094
	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	Ranked	Subtracted	232.601	244.534	11.933
	synapsin i (brain protein 4.1). [swissprot;acc:p17600]		Divided	229.072	216.576	1.0577
	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	Squared		18548.7	21798.2	1.17519
670	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	Rooted	Subtracted	49.8325	45.2077	4.6248
	autoantigen ngp-1. [swissprot;acc:q13823]	Ranked	Divided	250.302	236.817	1.05694
	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]	Measured	Subtracted	10075.5	9377.75	697.75
	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]	Squared		25911.5	30281.9	4370.4
	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	Rooted	Divided	51.2122	47.5637	1.07671

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.