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

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Showing element 123 to 172 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison
16	ATPBD1C	protein x 0004. [refseq;acc:nm_016301]	Measured	Divided	2671	871	3.06659
			Squared		1688.58	179.56	9.40399
	GNG8	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Ranked	Subtracted	266.864	336.184	69.32
	MAGEA6	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Squared		219048	129762	89286
	MAP1LC3A	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Ranked	Divided	56.7252	75.3954	1.32913
	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Rooted		51.6817	29.5127	1.75117
17	ATG4B	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Ranked		56.7841	75.447	1.32866
	ATPBD1C	protein x 0004. [refseq;acc:nm_016301]	Rooted		51.6817	29.5127	1.75117
	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Measured		460	1365	2.96739
			Squared		50.0828	441	8.80542
	GNG5	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Ranked	Subtracted	266.864	336.182	69.318
	MAP1LC3B	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Measured		24255.7	18168.9	6086.8
	NDN	necdin. [swissprot;acc:q99608]	Squared		219048	129762	89286
	PSCD1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Rooted		203.673	182.638	21.035
18	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		Divided	21.4476	36.9459	1.72261
	GBE1	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Ranked		185.678	245.247	1.32082
	GNG10	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]		Subtracted	266.865	336.181	69.316
	MAGED1	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Squared		219048	129762	89286
	MAP1LC3A	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Measured		24255.7	18168.9	6086.8
	PPP1R14A	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
			Squared		108.641	823.69	7.58176
	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Rooted	Subtracted	203.673	182.638	21.035
19	no value	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Ranked		266.865	336.178	69.313
	ATG4B	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured		24250	18164.9	6085.1
	MAGEF1	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Squared		219048	129762	89286
	MFAP4	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Measured	Divided	677.5	1865.5	2.75351
			Squared		108.641	823.69	7.58176
	PRKRAP1	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Rooted		25.6987	43.561	1.69507
	PSCD4	cytohesin 4. [swissprot;acc:q9uia0]		Subtracted	203.673	182.638	21.035
	PYGB	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Ranked	Divided	185.678	245.247	1.32082
20	no value	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Rooted		40.3337	24.2744	1.66157
	GABARAP	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured	Subtracted	23421.5	17580.4	5841.1
	GNG11	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Ranked		266.868	336.159	69.291
	MAGEB6B	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Squared		219048	129762	89286
	PPP1R14D	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Measured	Divided	677.5	1865.5	2.75351
			Squared		108.641	823.69	7.58176
	PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Rooted	Subtracted	203.673	182.638	21.035
	PYGL	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Ranked	Divided	185.678	245.247	1.32082
21	no value	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Squared	Subtracted	219048	129762	89286
	ATG4A	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Rooted		153.602	133.195	20.407
	FCN2	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Measured	Divided	677.5	1865.5	2.75351
			Squared		108.641	823.69	7.58176
	GNG12	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Rooted		40.3337	24.2744	1.66157
	MAGED4	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Measured	Subtracted	23693.7	18263	5430.7
	MYO15A	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Ranked	Divided	185.678	245.247	1.32082
	TMEM132A	gbp protein isoform a. [refseq;acc:nm_017870]		Subtracted	325.586	256.492	69.094
22	no value	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Measured	Divided	677.5	1865.5	2.75351
			Squared		108.641	823.69	7.58176
	GNG4	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Rooted		40.3357	24.2915	1.66049
	MAGEA9	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Squared	Subtracted	219048	129762	89286

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
- Hugo is the HGNC identifier if it exists
- 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.