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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 38536 in total

Value Type	Measured
Network Comparison Type	Divided

Rank	Filtered	description	Interaction Map	red	green	network_comparison	
13	1	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	High confidence	398.5	1281.5	3.21581	
13	1	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [source:refseq;acc:nm_018433]	Low confidence	1927.68	2959.19	1.5351	
14	0	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	High confidence	130.512	6.50325	20.0687	
14	0	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	0.00001	59	5900000	
14	1	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	High confidence	398.5	1281.5	3.21581	
14	1	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [source:swissprot;acc:p35030]	Low confidence	1972.65	2998.1	1.51983	
15	0	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	Low confidence	485.286	2740.13	5.64642	
15	0	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	10	156	15.6	
15	1	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [source:swissprot;acc:p07477]	Low confidence	1983.91	3007.85	1.51612	
15	1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	High confidence	2671	871	3.06659	
16	0	protein kinase, lysine deficient 3. [source:refseq;acc:nm_020922]	Low confidence	125	704.5	5.636	
16	0	protein transport protein sec24c (sec24-related protein c). [source:swissprot;acc:p53992]	High confidence	1	15	15	
16	1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Low confidence	21185	28492	1.34491	
16	1	protein x 0004. [source:refseq;acc:nm_016301]	High confidence	2671	871	3.06659	
17	0	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	High confidence	859	58	14.8103	
17	0	ptd016 protein. [source:refseq;acc:nm_016125]	Low confidence	30	158	5.26667	
17	1	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	High confidence	460	1365	2.96739	
17	1	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Low confidence	21185	28492	1.34491	
18	0	60s ribosomal protein l37a. [source:swissprot;acc:p12751]	High confidence	305.45	26.1599	11.6763	
18	0	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [source:swissprot;acc:p56211]	Low confidence	99	19	5.21053	
18	1	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Low confidence	5492.04	7251	1.32027	
18	1	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	High confidence	677.5	1865.5	2.75351	
19	0	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	305.45	26.1599	11.6763	
19	0	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	153	662	4.3268	
19	1	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	3032.56	3915.4	1.29112	
19	1	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	High confidence	677.5	1865.5	2.75351	
20	0	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [source:refseq;acc:nm_031938]	Low confidence	570	139	4.10072	
20	0	ero1-like. [source:refseq;acc:nm_014584]	High confidence	82	0.00001	8200000	
20	1	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	High confidence	677.5	1865.5	2.75351	
20	1	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Low confidence	7256.71	9368.87	1.29106	
21	0	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	111.278	434.911	3.90833	
21	0	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	High confidence	118.878	17.6611	6.73106	
21	1	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	3035.43	3917.88	1.29072	
21	1	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	677.5	1865.5	2.75351	
22	0	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	37	0.00001	3700000	
22	0	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	High confidence	60	0.00001	6000000	
22	1	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	3126.88	3997.02	1.27828	
22	1	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	677.5	1865.5	2.75351	
23	0	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [source:refseq;acc:nm_004267]	Low confidence	37	0.00001	3700000	
23	0	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	0.00001	59	5900000	
23	1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Low confidence	40899	32028.5	1.27696	
23	1	gbp protein isoform a. [source:refseq;acc:nm_017870]	High confidence	699.76	1894.39	2.7072	
24	0	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [source:swissprot;acc:q9ubr2]	Low confidence	154	493	3.2013	
24	0	ptd016 protein. [source:refseq;acc:nm_016125]	High confidence	30	158	5.26667	
24	1	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Low confidence	5720.25	4577.5	1.24965	
24	1	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	High confidence	950.561	2108.52	2.21818	
25	0	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	Low confidence	12.6208	39.8063	3.15402	
25	0	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	High confidence	148	773	5.22297	
25	1	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	High confidence	1833.01	892.67	2.0534	
25	1	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	5847.46	4691.96	1.24627	

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/