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	Network Comparison Type	Interaction Map	Value Type	red	network_comparison	Filtered	green

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Showing element 1 to 50 of 3730 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Value Type  : Ranked

Rank	description	red	network_comparison	Filtered	green
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294	3.70633	0	15915
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10	2.4	1	24
2	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	15	1.86667		28
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	2.55362	0	14977
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	15	1.86667	1	28
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	4475.84	2.47638	0	11083.9
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	15	1.86667	1	28
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906	2.45711	0	21883
5	cytohesin 4. [swissprot;acc:q9uia0]	15	1.86667	1	28
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	5510.5	2.17144	0	11965.7
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	15	1.86667	1	28
	ubiquitin protein ligase. [refseq;acc:nm_130466]	7523	2.03897	0	15339.2
7	cab2. [refseq;acc:nm_033419]	21866	1.99689		10950
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	1.49767	1	322
8	hbs1-like. [refseq;acc:nm_006620]
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	11525	1.89918	0	21888
9	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	212	1.45755	1	309
10	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	7509.39	1.88805	0	14178.1
	protein x 0004. [refseq;acc:nm_016301]	212	1.45755	1	309
11	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	11627	1.86092	0	6248
	rad50-interacting protein 1. [refseq;acc:nm_021930]	337	1.45259	1	232
12	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	9429.18	1.81023	0	5208.84
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	337	1.45259	1	232
13	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	5210.5	1.77804	0	9264.5
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	288.754	1.3585	1	212.554
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	56.6768	1.32952		75.3531
	dystrophin. [swissprot;acc:p11532]	10232.5	1.76446	0	18054.8
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	56.7244	1.32914	1	75.3948
	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	19403	1.72211	0	11267
16	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	12170.7	1.69839		20670.6
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	56.7252	1.32913	1	75.3954
17	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	56.7841	1.32866		75.447
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	11543	1.69451	0	6812
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	185.678	1.32082	1	245.247
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	22286	1.68629	0	13216
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	185.678	1.32082	1	245.247
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	22286	1.68629	0	13216
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	185.678	1.32082	1	245.247
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	22286	1.68629	0	13216
21	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	6313.38	1.68236		10621.4
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	185.678	1.32082	1	245.247
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	20989	1.68195	0	12479
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	58	1.31818	1	44
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	15520.4	1.67148	0	9285.44
24	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	13730.5	1.66289		8257
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	58	1.31818	1	44
25	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	13730.5	1.66289	0	8257
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	58	1.31818	1	44

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.