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	green	red	network_comparison

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

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.