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	Network Comparison Type	Interaction Map	network_comparison	Rank	description	green	red

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Showing element 3180 to 3229 of 77072 in total

Filtered  : 0
Value Type  : Ranked
Network Comparison Type  : Divided

Interaction Map	network_comparison	Rank	description	green	red
High confidence	1.77804	13	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	9264.5	5210.5
	1.81023	12	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	5208.84	9429.18
	1.86092	11	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	6248	11627
	1.88805	10	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	14178.1	7509.39
	1.89918	8	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	21888	11525
		9	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	1.99689	7	cab2. [refseq;acc:nm_033419]	10950	21866
	2.03897	6	ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2	7523
	2.17144	5	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7	5510.5
	2.45711	4	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	8906
	2.47638	3	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	4475.84
	2.55362	2	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	5865
	3.70633	1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	4294
Low confidence	1	837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]	0.00001	0.00001
		838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
		839	cobw-like protein. [refseq;acc:nm_018491]
		840	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	394	394
		841	gamma-glutamyltransferase. [sptrembl;acc:q14390]	0.00001	0.00001
		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]
	1.00007	836	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	13844.1	13845
	1.00032	835	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	11478.8	11482.5
	1.00041	834	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	16322.5	16315.8
	1.00078	833	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	12904.6	12894.5
	1.00094	831	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	11872.8	11861.6
		832	vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]	2668.83	2671.33
	1.00133	830	scratch; scratch 1. [refseq;acc:nm_031309]	12881.3	12864.2
	1.00149	829	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	11085.2	11101.7
	1.00161	828	lactotransferrin precursor (lactoferrin) [contains: lactoferroxin a; lactoferroxin b; lactoferroxin c]. [swissprot;acc:p02788]	13860.3	13838
	1.00168	827	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683]	8221.19	8207.37
	1.00173	826	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	11255.5	11236.1
	1.00181	825	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	11854.2	11832.8
	1.00185	824	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	12035.6	12057.9
	1.00189	821	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	11194.8	11173.7
		822	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]
		823	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]
	1.00195	820	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	11119.5	11097.9
	1.002	819	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	11256.8	11234.3
	1.00223	818	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	10615	10591.4
	1.00241	817	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	12473.9	12443.9
	1.00244	816	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	11333.4	11305.8
	1.00317	815	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	11985.2	12023.2
	1.00318	814	casein kinase i alpha s-like. [refseq;acc:nm_145203]	12971.5	13012.7
	1.00328	813	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	14231.9	14278.6
	1.00373	812	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	11786.9	11743.1
	1.00377	811	cervical cancer 1 protooncogene protein p40; regulator of tp53. [refseq;acc:nm_015416]	3724	3710
	1.00402	810	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	10637.6	10680.4
	1.00403	809	histone h4. [swissprot;acc:p02304]	11720.2	11673.1
	1.00406	808	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	10646.1	10603
	1.00408	807	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	8165.74	8132.58

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.