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

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Showing element 1 to 50 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	network_comparison	red	green
1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Subtracted	107	215	322
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	2.4	10	24
2	hbs1-like. [refseq;acc:nm_006620]	Subtracted	107	215	322
	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]	Divided	1.86667	15	28
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted	105	337	232
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Divided	1.86667	15	28
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Subtracted	105	337	232
5	cytohesin 4. [swissprot;acc:q9uia0]	Divided	1.86667	15	28
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Subtracted	97	212	309
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Divided	1.86667	15	28
	protein x 0004. [refseq;acc:nm_016301]	Subtracted	97	212	309
7	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	1.49767	215	322
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted	76.2	288.754	212.554
8	hbs1-like. [refseq;acc:nm_006620]	Divided	1.49767	215	322
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Subtracted	74	288	362
9	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	1.45755	212	309
10	protein x 0004. [refseq;acc:nm_016301]
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Subtracted	74	288	362
11	db83 protein. [swissprot;acc:p57088]
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	1.45259	337	232
12	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Subtracted	69.377	266.856	336.233
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	1.45259	337	232
13	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Subtracted	69.377	266.856	336.233
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Divided	1.3585	288.754	212.554
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		1.32952	56.6768	75.3531
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Subtracted	69.328	266.863	336.191
15	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]		69.327		336.19
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Divided	1.32914	56.7244	75.3948
16	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Subtracted	69.32	266.864	336.184
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Divided	1.32913	56.7252	75.3954
17	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]		1.32866	56.7841	75.447
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Subtracted	69.318	266.864	336.182
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Divided	1.32082	185.678	245.247
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Subtracted	69.316	266.865	336.181
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Divided	1.32082	185.678	245.247
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Subtracted	69.313	266.865	336.178
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Divided	1.32082	185.678	245.247
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Subtracted	69.291	266.868	336.159
21	gbp protein isoform a. [refseq;acc:nm_017870]		69.094	325.586	256.492
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Divided	1.32082	185.678	245.247
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Subtracted	69	322	253
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Divided	1.31818	58	44
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Subtracted	69	322	253
24	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Divided	1.31818	58	44
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Subtracted	69	322	253
25	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Divided	1.31818	58	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.