Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 Rank Gene description green Network Comparison Type Interaction Map red network_comparison

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Showing element 1 to 50 of 38536 in total

Filtered	0
Value Type	Measured
Network Comparison Type	Divided

Rank	description	green	Interaction Map	red	network_comparison	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	0.00001	High confidence	364	36400000	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	0.00001	Low confidence	364	36400000	
2	cab2. [source:refseq;acc:nm_033419]	174	High confidence	0.00001	17400000	
2	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	89	Low confidence	0.00001	8900000	
3	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	89	Low confidence	0.00001	8900000	
3	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	109	High confidence	0.00001	10900000	
4	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	89	Low confidence	0.00001	8900000	
4	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	89	High confidence	0.00001	8900000	
5	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	89	High confidence	0.00001	8900000	
5	jumonji protein. [source:swissprot;acc:q92833]	17.5166	Low confidence	0.00001	1751660	
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	89	High confidence	0.00001	8900000	
6	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	0.00001	Low confidence	13	1300000	
7	sedlin. [source:swissprot;acc:o14582]	43	High confidence	0.00001	4300000	
7	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [source:refseq;acc:nm_007063]	0.00001	Low confidence	2.31962	231962	
8	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	6410	Low confidence	85	75.4118	
8	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	43	High confidence	0.00001	4300000	
9	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	6410	High confidence	85	75.4118	
9	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [source:swissprot;acc:o14607]	10.6048	Low confidence	383.762	36.1876	
10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	6410	High confidence	85	75.4118	
10	serpin b12. [source:swissprot;acc:q96p63]	5.56738	Low confidence	199.549	35.8425	
11	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	5.71669	Low confidence	199.249	34.8539	
11	serpin b12. [source:swissprot;acc:q96p63]	5.56738	High confidence	199.549	35.8425	
12	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	5.71669	High confidence	199.249	34.8539	
12	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	58	Low confidence	859	14.8103	
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	47	High confidence	1363	29	
13	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). [source:swissprot;acc:o75344]	115.385	Low confidence	8.11997	14.21	
14	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	6.50325	High confidence	130.512	20.0687	
14	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). [source:swissprot;acc:q9byb4]	59	Low confidence	0.00001	5900000	
15	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	2740.13	Low confidence	485.286	5.64642	
15	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	156	High confidence	10	15.6	
16	protein kinase, lysine deficient 3. [source:refseq;acc:nm_020922]	704.5	Low confidence	125	5.636	
16	protein transport protein sec24c (sec24-related protein c). [source:swissprot;acc:p53992]	15	High confidence	1	15	
17	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	58	High confidence	859	14.8103	
17	ptd016 protein. [source:refseq;acc:nm_016125]	158	Low confidence	30	5.26667	
18	60s ribosomal protein l37a. [source:swissprot;acc:p12751]	26.1599	High confidence	305.45	11.6763	
18	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [source:swissprot;acc:p56211]	19	Low confidence	99	5.21053	
19	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	26.1599	High confidence	305.45	11.6763	
19	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402]	662	Low confidence	153	4.3268	
20	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [source:refseq;acc:nm_031938]	139	Low confidence	570	4.10072	
20	ero1-like. [source:refseq;acc:nm_014584]	0.00001	High confidence	82	8200000	
21	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	434.911	Low confidence	111.278	3.90833	
21	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	17.6611	High confidence	118.878	6.73106	
22	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [source:refseq;acc:nm_021615]	0.00001	Low confidence	37	3700000	
22	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	0.00001	High confidence	60	6000000	
23	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [source:refseq;acc:nm_004267]	0.00001	Low confidence	37	3700000	
23	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). [source:swissprot;acc:q9byb4]	59	High confidence	0.00001	5900000	
24	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [source:swissprot;acc:q9ubr2]	493	Low confidence	154	3.2013	
24	ptd016 protein. [source:refseq;acc:nm_016125]	158	High confidence	30	5.26667	
25	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	39.8063	Low confidence	12.6208	3.15402	
25	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	773	High confidence	148	5.22297	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/