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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1030 to 1079 of 29840 in total

Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison	
65	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Ranked	Divided	1	267.136	336.077	1.25807	
65	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Squared	Divided	1	219048	129762	1.68808	
65	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	Rooted	Subtracted	1	137.446	120.823	16.623	
65	metaxin 1. [source:swissprot;acc:q13505]	Squared	Subtracted	0	6149.89	3429.64	2720.25	
65	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Squared	Subtracted	1	144912	81155	63757	
65	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Measured	Subtracted	0	420.365	861.814	441.449	
65	neuralized-like. [source:refseq;acc:nm_004210]	Measured	Divided	1	1657.68	2690.25	1.6229	
65	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Ranked	Subtracted	0	8519.83	11453	2933.17	
65	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Measured	Divided	0	18	0.00001	1800000	
65	sedlin. [source:swissprot;acc:o14582]	Rooted	Subtracted	0	0	6.55744	6.55744	
65	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [source:swissprot;acc:q00007]	Ranked	Subtracted	1	187.457	243.678	56.221	
66	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Measured	Subtracted	1	17757.5	14008	3749.5	
66	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Squared	Divided	0	1797.76	558.241	3.2204	
66	fibrillin 3. [source:refseq;acc:nm_032447]	Measured	Subtracted	0	14246	13809	437	
66	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Rooted	Divided	1	63.8686	47.2654	1.35128	
66	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Ranked	Divided	1	267.136	336.077	1.25807	
66	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	Ranked	Divided	0	11461	15180	1.32449	
66	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Squared	Divided	1	219048	129762	1.68808	
66	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Squared	Subtracted	1	144911	81154.7	63756.3	
66	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [source:swissprot;acc:q16718]	Ranked	Subtracted	0	9830	6909	2921	
66	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Measured	Divided	1	1991.03	3221.38	1.61795	
66	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Rooted	Divided	0	30.9855	21.9983	1.40854	
66	soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	Measured	Divided	0	688.436	385.626	1.78524	
66	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Rooted	Subtracted	0	0	6.55744	6.55744	
66	trophinin. [source:swissprot;acc:q12816]	Rooted	Subtracted	1	137.446	120.823	16.623	
66	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [source:swissprot;acc:p23258]	Squared	Subtracted	0	8660.1	5963.73	2696.37	
66	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Ranked	Subtracted	1	187.458	243.678	56.22	
67	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Rooted	Subtracted	1	63.8686	47.2654	16.6032	
67	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Measured	Divided	1	6475.5	10307.5	1.59177	
67	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Squared	Subtracted	1	144876	81136.5	63739.5	
67	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Measured	Divided	0	1603	898	1.78508	
67	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Squared	Divided	0	608.191	190.865	3.1865	
67	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	Ranked	Divided	1	267.14	336.075	1.25805	
67	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	Rooted	Divided	0	11.0051	15.3166	1.39177	
67	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Squared	Divided	1	219048	129762	1.68808	
67	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Rooted	Divided	1	63.8686	47.2654	1.35128	
67	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Rooted	Subtracted	0	7.90063	14.4058	6.50517	
67	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [source:refseq;acc:nm_172341]	Ranked	Divided	0	10793.5	14291.5	1.32408	
67	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [source:swissprot;acc:p00491]	Measured	Subtracted	0	4755.32	4320.09	435.23	
67	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [source:swissprot;acc:p00491]	Ranked	Subtracted	0	8932.56	11823.3	2890.74	
67	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Measured	Subtracted	1	17756.5	14007.3	3749.2	
67	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [source:swissprot;acc:q00005]	Ranked	Subtracted	1	187.458	243.677	56.219	
67	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [source:swissprot;acc:o75795]	Squared	Subtracted	0	6123.28	3763.18	2360.1	
68	40s ribosomal protein s26. [source:swissprot;acc:p02383]	Ranked	Subtracted	0	14269.7	17098	2828.3	
68	alpha crystallin a chain. [source:swissprot;acc:p02489]	Rooted	Divided	0	6.22183	8.63381	1.38766	
68	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Measured	Divided	1	6475.5	10307.5	1.59177	
68	cyclin g2. [source:swissprot;acc:q16589]	Measured	Subtracted	1	17738.6	13995.7	3742.9	
68	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [source:swissprot;acc:q05932]	Measured	Subtracted	0	6452.66	6019.79	432.87	
68	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Squared	Subtracted	1	139741	78454.6	61286.4	
68	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Rooted	Subtracted	1	63.8686	47.2654	16.6032	

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/