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

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Showing element 1 to 50 of 7460 in total

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

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

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.