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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Filtered	Value Type	Network Comparison Type	Gene	Interaction Map	Rank	network_comparison	description	green	red

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Showing element 501 to 550 of 77072 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided

Interaction Map	Rank	network_comparison	description	green	red
High confidence	501	1	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]	0.00001	0.00001
	502		brca1 associated protein. [refseq;acc:nm_006768]
Low confidence	1	36400000	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		364
	2	8900000	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	0.00001
	3		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	4		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
	5	1751660	jumonji protein. [swissprot;acc:q92833]	17.5166
	6	1300000	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001	13
	7	231962	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]		2.31962
	8	75.4118	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	85
	9	36.1876	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	10.6048	383.762
	10	35.8425	serpin b12. [swissprot;acc:q96p63]	5.56738	199.549
	11	34.8539	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669	199.249
	12	14.8103	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	58	859
	13	14.21	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	115.385	8.11997
	14	5900000	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	59	0.00001
	15	5.64642	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	2740.13	485.286
	16	5.636	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	704.5	125
	17	5.26667	ptd016 protein. [refseq;acc:nm_016125]	158	30
	18	5.21053	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	19	99
	19	4.3268	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	662	153
	20	4.10072	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	139	570
	21	3.90833	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	434.911	111.278
	22	3700000	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	0.00001	37
	23		carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
	24	3.2013	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	493	154
	25	3.15402	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	39.8063	12.6208
	26	3.04255	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	47	143
	27	2.97183	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	35.5	105.5
	28		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
	29		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
	30		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
	31		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
	32		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
	33		melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
	34		melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
	35		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
	36		melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
	37		melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
	38		melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
	39		melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
	40		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
	41		melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
	42		melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
	43		melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
	44	28600000	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	0.00001	286
	45		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
	46	2.79167	ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760]	67	24
	47	2.50526	tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105]	776.89	310.103
	48	2.42708	pnas-129. [sptrembl;acc:q9bxv8]	151.073	366.666

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.