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 1991 to 2040 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1991	transcriptional co-activator with pdz-binding motif (taz). [source:refseq;acc:nm_015472]	219.26	217.194	1.00951	
1992	zasp protein (fragment). [source:sptrembl;acc:q9y4z3]	219.267	217.207	1.00948	
1993	huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	189.052	190.835	1.00943	
1994	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [source:swissprot;acc:q9y5p4]	189.011	190.787	1.0094	
1995	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	188.961	190.73	1.00936	
1996	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [source:swissprot;acc:q92911]	204.682	202.784	1.00936	
1997	kidney and liver proline oxidase 1. [source:refseq;acc:nm_021232]	204.651	202.759	1.00933	
1998	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	200.219	198.37	1.00932	
1999	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [source:refseq;acc:nm_145913]	204.636	202.748	1.00931	
2000	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [source:swissprot;acc:q9y289]	204.626	202.739	1.00931	
2001	lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [source:refseq;acc:nm_022165]	225.02	222.948	1.00929	
2002	u2 small nuclear ribonucleoprotein b". [source:swissprot;acc:p08579]	214.775	216.769	1.00928	
2003	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [source:swissprot;acc:o14645]	208.315	206.41	1.00923	
2004	receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [source:swissprot;acc:q15303]	225.019	222.969	1.00919	
2005	epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [source:swissprot;acc:p00533]	225.019	222.971	1.00919	
2006	receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [source:swissprot;acc:p04626]	225.019	222.971	1.00919	
2007	2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [source:swissprot;acc:q9uj83]	225.019	222.969	1.00919	
2008	receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [source:swissprot;acc:p21860]	225.019	222.969	1.00919	
2009	proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [source:swissprot;acc:p40306]	216.201	214.245	1.00913	
2010	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [source:swissprot;acc:q15814]	193.517	191.766	1.00913	
2011	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [source:swissprot;acc:q9y305]	193.517	191.766	1.00913	
2012	dead-box protein. [source:refseq;acc:nm_018665]	193.517	191.766	1.00913	
2013	protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [source:refseq;acc:nm_002481]	217.662	215.693	1.00913	
2014	protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [source:refseq;acc:nm_002480]	217.676	215.709	1.00912	
2015	dna topoisomerase iii alpha (ec 5.99.1.2). [source:swissprot;acc:q13472]	217.941	215.979	1.00908	
2016	electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [source:swissprot;acc:q16134]	199.092	197.301	1.00908	
2017	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	127.397	128.553	1.00907	
2018	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	127.397	128.553	1.00907	
2019	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [source:swissprot;acc:p45954]	215.799	213.865	1.00904	
2020	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [source:swissprot;acc:o75153]	223.168	221.176	1.00901	
2021	hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [source:swissprot;acc:q9nzj6]	208.601	210.464	1.00893	
2022	atp synthase coupling factor b, mitochondrial precursor. [source:swissprot;acc:q99766]	208.601	210.464	1.00893	
2023	guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [source:swissprot;acc:q9y2t3]	208.601	210.464	1.00893	
2024	vacuolar protein sorting 33b (hvps33b). [source:swissprot;acc:q9h267]	215.553	213.663	1.00885	
2025	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [source:swissprot;acc:p24298]	189.987	191.668	1.00885	
2026	vacuolar protein sorting 11 (hvps11) (pp3476). [source:swissprot;acc:q9h270]	215.553	213.663	1.00885	
2027	lin-7 homolog c; lin-7 protein 3. [source:refseq;acc:nm_018362]	225.015	223.041	1.00885	
2028	vacuolar protein sorting 33a (hvps33a). [source:swissprot;acc:q96ax1]	215.553	213.663	1.00885	
2029	cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [source:refseq;acc:nm_004059]	189.999	191.677	1.00883	
2030	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [source:refseq;acc:nm_133443]	189.999	191.677	1.00883	
2031	traf and tnf receptor-associated protein; ets1-associated protein 2. [source:refseq;acc:nm_016614]	218.466	216.562	1.00879	
2032	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [source:swissprot;acc:q96kx2]	215.322	213.46	1.00872	
2033	f-actin capping protein beta subunit (capz beta). [source:swissprot;acc:p47756]	215.322	213.46	1.00872	
2034	centaurin beta 5 (cnt-b5). [source:swissprot;acc:q96p50]	218.919	220.812	1.00865	
2035	centaurin beta 2 (cnt-b2). [source:swissprot;acc:q15057]	218.919	220.812	1.00865	
2036	lamin b1. [source:swissprot;acc:p20700]	218.919	220.813	1.00865	
2037	centaurin beta 1 (cnt-b1). [source:swissprot;acc:q15027]	218.919	220.812	1.00865	
2038	lamin a/c (70 kda lamin). [source:swissprot;acc:p02545]	218.92	220.811	1.00864	
2039	acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [source:swissprot;acc:q9nr19]	190.551	192.191	1.00861	
2040	brachyury protein (t protein). [source:swissprot;acc:o15178]	210.586	208.803	1.00854	

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/