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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 9634 in total 
Value Type	Measured
Network Comparison Type	Divided

Rank	description	Interaction Map	Filtered	red	green	network_comparison	
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]	Low confidence	0	8.11997	115.385	14.21	
13	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [source:refseq;acc:nm_018433]	Low confidence	1	1927.68	2959.19	1.5351	
14	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	High confidence	0	130.512	6.50325	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]	Low confidence	0	0.00001	59	5900000	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	High confidence	1	398.5	1281.5	3.21581	
14	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [source:swissprot;acc:p35030]	Low confidence	1	1972.65	2998.1	1.51983	
15	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	Low confidence	0	485.286	2740.13	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]	High confidence	0	10	156	15.6	
15	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [source:swissprot;acc:p07477]	Low confidence	1	1983.91	3007.85	1.51612	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	High confidence	1	2671	871	3.06659	
16	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Low confidence	1	21185	28492	1.34491	
16	protein kinase, lysine deficient 3. [source:refseq;acc:nm_020922]	Low confidence	0	125	704.5	5.636	
16	protein transport protein sec24c (sec24-related protein c). [source:swissprot;acc:p53992]	High confidence	0	1	15	15	
16	protein x 0004. [source:refseq;acc:nm_016301]	High confidence	1	2671	871	3.06659	
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	High confidence	1	460	1365	2.96739	
17	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Low confidence	1	21185	28492	1.34491	
17	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	High confidence	0	859	58	14.8103	
17	ptd016 protein. [source:refseq;acc:nm_016125]	Low confidence	0	30	158	5.26667	
18	60s ribosomal protein l37a. [source:swissprot;acc:p12751]	High confidence	0	305.45	26.1599	11.6763	
18	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [source:swissprot;acc:p56211]	Low confidence	0	99	19	5.21053	
18	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Low confidence	1	5492.04	7251	1.32027	
18	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	High confidence	1	677.5	1865.5	2.75351	
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]	High confidence	0	305.45	26.1599	11.6763	
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]	Low confidence	1	3032.56	3915.4	1.29112	
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]	Low confidence	0	153	662	4.3268	
19	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	High confidence	1	677.5	1865.5	2.75351	
20	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [source:refseq;acc:nm_031938]	Low confidence	0	570	139	4.10072	
20	ero1-like. [source:refseq;acc:nm_014584]	High confidence	0	82	0.00001	8200000	
20	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	High confidence	1	677.5	1865.5	2.75351	
20	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Low confidence	1	7256.71	9368.87	1.29106	
21	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [source:swissprot;acc:q02318]	Low confidence	1	3035.43	3917.88	1.29072	
21	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [source:swissprot;acc:q15485]	High confidence	1	677.5	1865.5	2.75351	
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]	Low confidence	0	111.278	434.911	3.90833	
21	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	High confidence	0	118.878	17.6611	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]	Low confidence	0	37	0.00001	3700000	
22	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [source:swissprot;acc:q07973]	Low confidence	1	3126.88	3997.02	1.27828	
22	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	High confidence	1	677.5	1865.5	2.75351	
22	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	High confidence	0	60	0.00001	6000000	
23	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [source:refseq;acc:nm_004267]	Low confidence	0	37	0.00001	3700000	
23	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Low confidence	1	40899	32028.5	1.27696	
23	gbp protein isoform a. [source:refseq;acc:nm_017870]	High confidence	1	699.76	1894.39	2.7072	
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]	High confidence	0	0.00001	59	5900000	
24	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Low confidence	1	5720.25	4577.5	1.24965	
24	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [source:swissprot;acc:q9ubr2]	Low confidence	0	154	493	3.2013	
24	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	High confidence	1	950.561	2108.52	2.21818	
24	ptd016 protein. [source:refseq;acc:nm_016125]	High confidence	0	30	158	5.26667	
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	High confidence	1	1833.01	892.67	2.0534	
25	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [source:swissprot;acc:p49773]	Low confidence	1	5847.46	4691.96	1.24627	
25	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	Low confidence	0	12.6208	39.8063	3.15402	
25	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	High confidence	0	148	773	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/