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	Interaction Map	Network Comparison Type	Filtered	red	network_comparison	green

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Showing element 82 to 131 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	Network Comparison Type	red	network_comparison	green
11	Measured	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted	21185	7307	28492
	Ranked	db83 protein. [swissprot;acc:p57088]		288	74	362
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	337	1.45259	232
	Squared	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]		37.5863	10.3414	388.696
		hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Subtracted	219048	89286	129762
	Rooted	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Divided	19.9625	1.79326	35.798
		protein x 0004. [refseq;acc:nm_016301]	Subtracted	51.6817	22.169	29.5127
12	Measured	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Divided	398.5	3.21581	1281.5
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	34190.9	6604.9	40795.8
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		266.856	69.377	336.233
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	337	1.45259	232
	Squared	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]		37.5863	10.3414	388.696
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Subtracted	219048	89286	129762
	Rooted	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]		80.4705	21.0555	101.526
		cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Divided	19.9625	1.79326	35.798
13	Measured	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]		398.5	3.21581	1281.5
		myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Subtracted	21591.5	6313	27904.5
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]		266.856	69.377	336.233
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Divided	288.754	1.3585	212.554
	Squared	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]		37.5863	10.3414	388.696
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Subtracted	219048	89286	129762
	Rooted	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		80.4705	21.0555	101.526
		cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Divided	19.9625	1.79326	35.798
14	Measured	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Subtracted	21591.5	6313	27904.5
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Divided	398.5	3.21581	1281.5
	Ranked	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		56.6768	1.32952	75.3531
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Subtracted	266.863	69.328	336.191
	Squared	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		219048	89286	129762
		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Divided	37.5863	10.3414	388.696
	Rooted			19.9625	1.79326	35.798
		spermatogenesis associated 6. [refseq;acc:nm_019073]	Subtracted	80.4705	21.0555	101.526
15	Measured	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]		21591.5	6313	27904.5
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	2671	3.06659	871
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Subtracted	266.863	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	56.7244	1.32914	75.3948
	Squared	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Subtracted	219048	89286	129762
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	1688.58	9.40399	179.56
	Rooted	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Subtracted	80.4705	21.0555	101.526
		gbp protein isoform a. [refseq;acc:nm_017870]	Divided	23.9771	1.77158	42.4773
16	Measured	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Subtracted	24260.3	6088.2	18172.1
		protein x 0004. [refseq;acc:nm_016301]	Divided	2671	3.06659	871
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Subtracted	266.864	69.32	336.184
		microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Divided	56.7252	1.32913	75.3954
	Squared	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Subtracted	219048	89286	129762
		protein x 0004. [refseq;acc:nm_016301]	Divided	1688.58	9.40399	179.56
	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	21.035	182.638
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	51.6817	1.75117	29.5127
17	Measured	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		460	2.96739	1365
		microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Subtracted	24255.7	6086.8	18168.9
	Ranked	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Divided	56.7841	1.32866	75.447

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.