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

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Showing element 2023 to 2072 of 3228 in total

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

Rank	description	red	green	network_comparison
2023	guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3]	208.601	210.464	1.00893
2024	vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]	215.553	213.663	1.00885
2025	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	189.987	191.668
2026	vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270]	215.553	213.663
2027	lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]	225.015	223.041
2028	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]	215.553	213.663
2029	cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059]	189.999	191.677	1.00883
2030	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]
2031	traf and tnf receptor-associated protein; ets1-associated protein 2. [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). [swissprot;acc:q96kx2]	215.322	213.46	1.00872
2033	f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
2034	centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]	218.919	220.812	1.00865
2035	centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
2036	lamin b1. [swissprot;acc:p20700]		220.813
2037	centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]		220.812
2038	lamin a/c (70 kda lamin). [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). [swissprot;acc:q9nr19]	190.551	192.191	1.00861
2040	brachyury protein (t protein). [swissprot;acc:o15178]	210.586	208.803	1.00854
2041	ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131]	196.808	195.141
2042	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	210.586	208.803
2043	ubiquilin 1 isoform 1. [refseq;acc:nm_013438]	196.837	195.173	1.00853
2044	adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203]	199.928	198.24	1.00851
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	solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3]	224.124	226.003	1.00838
2048	solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]
2049	translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770]	220.787	222.634	1.00837
2050	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	218.79	216.981	1.00834
2051	oxidation resistance 1. [refseq;acc:nm_181354]
2052	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	207.667	205.95
2053	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]	218.79	216.981
2054	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	207.665	205.948
2055	dymeclin. [refseq;acc:nm_017653]	218.79	216.981
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	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	207.638	205.923	1.00833
2064	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	207.655	205.939
2065	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]	214.328	212.561	1.00831
2066	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	229.102	231.001	1.00829
2067	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566]	193.226	191.639	1.00828
2068	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	220.8	222.61	1.0082
2069	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]	217.555	215.807	1.0081
2070	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	223.199	225.008
2071	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	217.555	215.807
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]

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.