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	Filtered	red	Interaction Map	network_comparison	green

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Showing element 101 to 150 of 38536 in total

Network Comparison Type  : Divided

Rank	Value Type	description	Filtered	red	Interaction Map	network_comparison	green
7	Ranked	cab2. [refseq;acc:nm_033419]	0	21866	High confidence	1.99689	10950
		fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]		11543	Low confidence	1.69451	6812
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	215	High confidence	1.49767	322
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]		318	Low confidence	1.325	240
	Squared	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	0.00001	High confidence	187479	1.87479
		jumonji protein. [swissprot;acc:q92833]			Low confidence	14096.2	0.140962
		oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	1	128.386		8.23493	1057.25
		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]		314.926	High confidence	11.544	27.2805
	Rooted	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	0	6.08276	Low confidence	608276	0.00001
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		0.00001	High confidence	943398	9.43398
		oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	1	27.1385	Low confidence	1.69401	45.9728
		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]		33.9632	High confidence	1.84327	18.4255
8	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	85	Low confidence	75.4118	6410
		db83 protein. [swissprot;acc:p57088]	1	1153.5	High confidence	3.39764	339.5
		phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]		3278	Low confidence	1.54317	5058.5
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	0.00001	High confidence	4300000	43
	Ranked	hbs1-like. [refseq;acc:nm_006620]	1	215		1.49767	322
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	22286	Low confidence	1.68629	13216
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		11525	High confidence	1.89918	21888
		oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	1	318	Low confidence	1.325	240
	Squared	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	1.73869		11098	19295.9
		db83 protein. [swissprot;acc:p57088]	1	314.926	High confidence	11.544	27.2805
		ero1-like. [refseq;acc:nm_014584]	0	1.59148		159148	0.00001
		phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	1	2543.26	Low confidence	2.38136	6056.43
	Rooted	db83 protein. [swissprot;acc:p57088]		33.9632	High confidence	1.84327	18.4255
		ero1-like. [refseq;acc:nm_014584]	0	9.05539		905539	0.00001
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		3.60555	Low confidence	360555
		thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	1	31.8641		1.49674	47.6922
9	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	85	High confidence	75.4118	6410
		n33 protein. [swissprot;acc:q13454]	1	3278	Low confidence	1.54317	5058.5
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]		398.5	High confidence	3.21581	1281.5
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	0	383.762	Low confidence	36.1876	10.6048
	Ranked	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1	58		1.31818	44
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	22286		1.68629	13216
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		11525	High confidence	1.89918	21888
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	212		1.45755	309
	Squared	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0	0.04	Low confidence	4000	0.00001
		n33 protein. [swissprot;acc:q13454]	1	2543.26		2.38136	6056.43
		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	0.852071	High confidence	85207.1	0.00001
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1	37.5863		10.3414	388.696
	Rooted	gbp protein isoform a. [refseq;acc:nm_017870]		31.8923	Low confidence	1.49599	47.7107
		jumonji protein. [swissprot;acc:q92833]	0	0.00001		300407	3.00407
		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		7.74597	High confidence	774597	0.00001
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1	19.9625		1.79326	35.798
10	Measured	implantation-associated protein. [refseq;acc:nm_032121]		3278	Low confidence	1.54317	5058.5
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	85	High confidence	75.4118	6410
		serpin b12. [swissprot;acc:q96p63]		199.549	Low confidence	35.8425	5.56738
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1	398.5	High confidence	3.21581	1281.5
	Ranked	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	0	7509.39		1.88805	14178.1
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		22286	Low confidence	1.68629	13216

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.