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

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Showing element 1 to 50 of 3730 in total

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

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