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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 9634 in total

Network Comparison Type

: Divided
Value Type

: Measured

Rank	description	Interaction Map	Filtered	red	network_comparison	green
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). [swissprot;acc:o75344]	Low confidence	0	8.11997	14.21	115.385
13	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Low confidence	1	1927.68	1.5351	2959.19
14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	High confidence	0	130.512	20.0687	6.50325
	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]	Low confidence	0	0.00001	5900000	59
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	High confidence	1	398.5	3.21581	1281.5
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Low confidence	1	1972.65	1.51983	2998.1
15	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Low confidence	0	485.286	5.64642	2740.13
	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). [swissprot;acc:o14521]	High confidence	0	10	15.6	156
	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	Low confidence	1	1983.91	1.51612	3007.85
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	High confidence		2671	3.06659	871
16	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Low confidence		21185	1.34491	28492
	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	Low confidence	0	125	5.636	704.5
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	High confidence	0	1	15	15
	protein x 0004. [refseq;acc:nm_016301]		1	2671	3.06659	871
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]			460	2.96739	1365
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Low confidence		21185	1.34491	28492
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	High confidence	0	859	14.8103	58
	ptd016 protein. [refseq;acc:nm_016125]	Low confidence		30	5.26667	158
18	60s ribosomal protein l37a. [swissprot;acc:p12751]	High confidence		305.45	11.6763	26.1599
	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	Low confidence		99	5.21053	19
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Low confidence	1	5492.04	1.32027	7251
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	High confidence	1	677.5	2.75351	1865.5
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). [swissprot;acc:o15528]	High confidence	0	305.45	11.6763	26.1599
		Low confidence	1	3032.56	1.29112	3915.4
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Low confidence	0	153	4.3268	662
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	High confidence	1	677.5	2.75351	1865.5
20	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Low confidence	0	570	4.10072	139
	ero1-like. [refseq;acc:nm_014584]	High confidence	0	82	8200000	0.00001
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	High confidence	1	677.5	2.75351	1865.5
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	Low confidence		7256.71	1.29106	9368.87
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). [swissprot;acc:q02318]	Low confidence		3035.43	1.29072	3917.88
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	High confidence		677.5	2.75351	1865.5
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Low confidence	0	111.278	3.90833	434.911
	syntaxin 10 (syn10). [swissprot;acc:o60499]	High confidence		118.878	6.73106	17.6611
22	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Low confidence		37	3700000	0.00001
	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	Low confidence	1	3126.88	1.27828	3997.02
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	High confidence	1	677.5	2.75351	1865.5
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	High confidence	0	60	6000000	0.00001
23	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Low confidence	0	37	3700000	0.00001
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Low confidence	1	40899	1.27696	32028.5
	gbp protein isoform a. [refseq;acc:nm_017870]	High confidence	1	699.76	2.7072	1894.39
	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]	High confidence	0	0.00001	5900000	59
24	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Low confidence	1	5720.25	1.24965	4577.5
	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	Low confidence	0	154	3.2013	493
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	High confidence	1	950.561	2.21818	2108.52
	ptd016 protein. [refseq;acc:nm_016125]		0	30	5.26667	158
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		1	1833.01	2.0534	892.67
	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773]	Low confidence	1	5847.46	1.24627	4691.96
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Low confidence	0	12.6208	3.15402	39.8063
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	High confidence	0	148	5.22297	773

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.

- http://analysis.yellowcouch.org/