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	red	green	network_comparison

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Showing element 101 to 150 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	Network Comparison Type	red	green	network_comparison
13	Squared	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Divided	37.5863	388.696	10.3414
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Subtracted	219048	129762	89286
	Rooted	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		80.4705	101.526	21.0555
		cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Divided	19.9625	35.798	1.79326
14	Measured	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Subtracted	21591.5	27904.5	6313
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Divided	398.5	1281.5	3.21581
	Ranked	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		56.6768	75.3531	1.32952
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Subtracted	266.863	336.191	69.328
	Squared	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		219048	129762	89286
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Divided	37.5863	388.696	10.3414
	Rooted			19.9625	35.798	1.79326
		spermatogenesis associated 6. [refseq;acc:nm_019073]	Subtracted	80.4705	101.526	21.0555
15	Measured	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]		21591.5	27904.5	6313
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	2671	871	3.06659
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Subtracted	266.863	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	56.7244	75.3948	1.32914
	Squared	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Subtracted	219048	129762	89286
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	1688.58	179.56	9.40399
	Rooted	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Subtracted	80.4705	101.526	21.0555
		gbp protein isoform a. [refseq;acc:nm_017870]	Divided	23.9771	42.4773	1.77158
16	Measured	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Subtracted	24260.3	18172.1	6088.2
		protein x 0004. [refseq;acc:nm_016301]	Divided	2671	871	3.06659
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Subtracted	266.864	336.184	69.32
		microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Divided	56.7252	75.3954	1.32913
	Squared	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Subtracted	219048	129762	89286
		protein x 0004. [refseq;acc:nm_016301]	Divided	1688.58	179.56	9.40399
	Rooted	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]	Subtracted	203.673	182.638	21.035
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	51.6817	29.5127	1.75117
17	Measured	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		460	1365	2.96739
		microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Subtracted	24255.7	18168.9	6086.8
	Ranked	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Divided	56.7841	75.447	1.32866
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Subtracted	266.864	336.182	69.318
	Squared	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Divided	50.0828	441	8.80542
		necdin. [swissprot;acc:q99608]	Subtracted	219048	129762	89286
	Rooted	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		203.673	182.638	21.035
		protein x 0004. [refseq;acc:nm_016301]	Divided	51.6817	29.5127	1.75117
18	Measured	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Subtracted	24255.7	18168.9	6086.8
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Divided	677.5	1865.5	2.75351
	Ranked	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]		185.678	245.247	1.32082
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Subtracted	266.865	336.181	69.316
	Squared	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]		219048	129762	89286
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Divided	108.641	823.69	7.58176
	Rooted	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Subtracted	203.673	182.638	21.035
		dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Divided	21.4476	36.9459	1.72261
19	Measured	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Subtracted	24250	18164.9	6085.1
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided	677.5	1865.5	2.75351
	Ranked	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]		185.678	245.247	1.32082
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Subtracted	266.865	336.178	69.313
	Squared	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]		219048	129762	89286
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided	108.641	823.69	7.58176

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.