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

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Showing element 2025 to 2074 of 3228 in total

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

Rank	green	description	network_comparison	red
2025	191.668	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	1.00885	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
2051		oxidation resistance 1. [refseq;acc:nm_181354]
2052	205.95	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]		207.667
2053	216.981	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]		218.79
2054	205.948	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]		207.665
2055	216.981	dymeclin. [refseq;acc:nm_017653]		218.79
2056		sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]
2057		lats homolog 1. [refseq;acc:nm_004690]
2058		sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
2059		nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]
2060		dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]
2061		tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]
2062		tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]
2063	205.923	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	1.00833	207.638
2064	205.939	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]		207.655
2065	212.561	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	1.00831	214.328
2066	231.001	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	1.00829	229.102
2067	191.639	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566]	1.00828	193.226
2068	222.61	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	1.0082	220.8
2069	215.807	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750]	1.0081	217.555
2070	225.008	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]		223.199
2071	215.807	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]		217.555
2072		dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]
2073	227.433	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	1.00806	229.267
2074	214.599	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098]	1.00804	216.324

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.