MK5 Microarray Data

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

Results: HTML CSV LaTeX

Showing element 2001 to 2050 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	green	description	network_comparison	red
2001	222.948	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). [refseq;acc:nm_022165]	1.00929	225.02
2002	216.769	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	1.00928	214.775
2003	206.41	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	1.00923	208.315
2004	222.969	receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303]	1.00919	225.019
2005	222.971	epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533]
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). [swissprot;acc:p04626]
2007	222.969	2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]
2008		receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860]
2009	214.245	proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306]	1.00913	216.201
2010	191.766	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814]		193.517
2011		putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
2012		dead-box protein. [refseq;acc:nm_018665]
2013	215.693	protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481]		217.662
2014	215.709	protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480]	1.00912	217.676
2015	215.979	dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472]	1.00908	217.941
2016	197.301	electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134]		199.092
2017	128.553	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	1.00907	127.397
2018		serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]
2019	213.865	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). [swissprot;acc:p45954]	1.00904	215.799
2020	221.176	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153]	1.00901	223.168
2021	210.464	hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6]	1.00893	208.601
2022		atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]
2023		guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3]
2024	213.663	vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]	1.00885	215.553
2025	191.668	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]		189.987
2026	213.663	vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270]		215.553
2027	223.041	lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]		225.015
2028	213.663	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]		215.553
2029	191.677	cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059]	1.00883	189.999
2030		alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]
2031	216.562	traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614]	1.00879	218.466
2032	213.46	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2]	1.00872	215.322
2033		f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
2034	220.812	centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]	1.00865	218.919
2035		centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
2036	220.813	lamin b1. [swissprot;acc:p20700]
2037	220.812	centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]
2038	220.811	lamin a/c (70 kda lamin). [swissprot;acc:p02545]	1.00864	218.92
2039	192.191	acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19]	1.00861	190.551
2040	208.803	brachyury protein (t protein). [swissprot;acc:o15178]	1.00854	210.586
2041	195.141	ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131]		196.808
2042	208.803	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]		210.586
2043	195.173	ubiquilin 1 isoform 1. [refseq;acc:nm_013438]	1.00853	196.837
2044	198.24	adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203]	1.00851	199.928
2045		ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]
2046		adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]
2047	226.003	solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3]	1.00838	224.124
2048		solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]
2049	222.634	translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770]	1.00837	220.787
2050	216.981	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	1.00834	218.79

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.