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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2132 to 2181 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
533	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [source:swissprot;acc:q92911]	Squared	28937.1	34588.8	1.19531	
534	40s ribosomal protein s16. [source:swissprot;acc:p17008]	Rooted	50.8036	46.8198	1.08509	
534	dehydrodolichyl diphosphate synthase. [source:refseq;acc:nm_024887]	Squared	27034.1	32301.8	1.19485	
534	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	Ranked	250.942	235.004	1.06782	
534	nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [source:refseq;acc:nm_012345]	Measured	4651.88	5296.78	1.13863	
535	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	Rooted	50.8041	46.8218	1.08505	
535	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [source:swissprot;acc:p52434]	Ranked	236.662	252.708	1.0678	
535	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [source:swissprot;acc:q13368]	Squared	37147.5	44372.1	1.19448	
535	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [source:swissprot;acc:p51571]	Measured	10603.5	12069.5	1.13826	
536	calsyntenin-1 precursor. [source:swissprot;acc:o94985]	Measured	10603.5	12069.5	1.13826	
536	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	Rooted	66.0815	71.6562	1.08436	
536	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [source:swissprot;acc:q9y287]	Squared	28657.6	34208.6	1.1937	
536	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Ranked	242.531	227.136	1.06778	
537	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	Rooted	66.0817	71.6545	1.08433	
537	integral membrane protein 2c (transmembrane protein bri3) (npd018). [source:swissprot;acc:q9nqx7]	Squared	28657.6	34208.6	1.1937	
537	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	Ranked	229.803	215.301	1.06736	
537	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]	Measured	10603.5	12069.5	1.13826	
538	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [source:swissprot;acc:p52436]	Ranked	237.627	253.604	1.06724	
538	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	Rooted	66.0817	71.6543	1.08433	
538	integral membrane protein 2a (e25 protein). [source:swissprot;acc:o43736]	Squared	28657.6	34208.6	1.1937	
538	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	Measured	10603.5	12069.4	1.13825	
539	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	Rooted	66.0818	71.6537	1.08432	
539	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	Ranked	236.964	252.86	1.06708	
539	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	Measured	10603.5	12069.4	1.13825	
539	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Squared	20613.1	24595.9	1.19322	
540	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	Squared	26048.6	31057.4	1.19229	
540	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	Rooted	66.082	71.6526	1.0843	
540	gk001 protein. [source:refseq;acc:nm_020198]	Measured	10603.5	12069.4	1.13825	
540	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Ranked	222.156	208.201	1.06703	
541	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	Measured	10600.3	12065.2	1.13819	
541	coatomer beta subunit (beta-coat protein) (beta-cop). [source:swissprot;acc:p53618]	Squared	53774.6	45105.5	1.1922	
541	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Ranked	222.156	208.201	1.06703	
541	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	Rooted	66.082	71.6526	1.0843	
542	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	Rooted	66.082	71.6526	1.0843	
542	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	Ranked	222.156	208.201	1.06703	
542	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [source:swissprot;acc:p31749]	Measured	3889.27	4426.74	1.13819	
542	s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [source:swissprot;acc:q00266]	Squared	26084.2	31084.3	1.19169	
543	calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	Measured	10599.9	12064.7	1.13819	
543	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	Rooted	66.082	71.6525	1.0843	
543	glutamate carboxypeptidase-like protein 2 precursor. [source:swissprot;acc:q96kn2]	Squared	26612.5	31709	1.19151	
543	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Ranked	222.156	208.201	1.06703	
544	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	Rooted	66.082	71.6525	1.0843	
544	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Ranked	222.156	208.201	1.06703	
544	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [source:swissprot;acc:q9y243]	Measured	3889.27	4426.74	1.13819	
544	ran binding protein 11. [source:refseq;acc:nm_016338]	Squared	26018.9	30994.1	1.19121	
545	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	Ranked	248.866	233.287	1.06678	
545	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	Rooted	66.082	71.6526	1.0843	
545	membrane protein expressed in epithelial-like lung adenocarcinoma. [source:refseq;acc:nm_024792]	Squared	26010	30981.7	1.19115	
545	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [source:swissprot;acc:p31751]	Measured	3889.27	4426.74	1.13819	
546	atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p30049]	Squared	27162.5	32347.5	1.19089	

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/