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	network_comparison	green

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Showing element 1 to 50 of 3730 in total

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

Rank	description	Filtered	red	network_comparison	green
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	4294	3.70633	15915
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	10	2.4	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]	0	5865	2.55362	14977
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	15	1.86667	28
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	0	4475.84	2.47638	11083.9
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	1	15	1.86667	28
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	8906	2.45711	21883
5	cytohesin 4. [swissprot;acc:q9uia0]	1	15	1.86667	28
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	0	5510.5	2.17144	11965.7
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	1	15	1.86667	28
	ubiquitin protein ligase. [refseq;acc:nm_130466]	0	7523	2.03897	15339.2
7	cab2. [refseq;acc:nm_033419]		21866	1.99689	10950
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	215	1.49767	322
8	hbs1-like. [refseq;acc:nm_006620]
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0	11525	1.89918	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]	1	212	1.45755	309
10	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	0	7509.39	1.88805	14178.1
	protein x 0004. [refseq;acc:nm_016301]	1	212	1.45755	309
11	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	0	11627	1.86092	6248
	rad50-interacting protein 1. [refseq;acc:nm_021930]	1	337	1.45259	232
12	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	0	9429.18	1.81023	5208.84
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	337	1.45259	232
13	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	0	5210.5	1.77804	9264.5
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	1	288.754	1.3585	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]	0	10232.5	1.76446	18054.8
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	1	56.7244	1.32914	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]	0	19403	1.72211	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]	1	56.7252	1.32913	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]	0	11543	1.69451	6812
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	1	185.678	1.32082	245.247
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	22286	1.68629	13216
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	1	185.678	1.32082	245.247
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	22286	1.68629	13216
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	1	185.678	1.32082	245.247
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	22286	1.68629	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]	1	185.678	1.32082	245.247
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	20989	1.68195	12479
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1	58	1.31818	44
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	0	15520.4	1.67148	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]	1	58	1.31818	44
25	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	13730.5	1.66289	8257
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	1	58	1.31818	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.