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	green	red	network_comparison

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Showing element 2025 to 2074 of 3228 in total

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

Rank	description	green	red	network_comparison
2025	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	191.668	189.987	1.00885
2026	vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270]	213.663	215.553
2027	lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]	223.041	225.015
2028	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]	213.663	215.553
2029	cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059]	191.677	189.999	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]	216.562	218.466	1.00879
2032	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2]	213.46	215.322	1.00872
2033	f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
2034	centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]	220.812	218.919	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]	220.811	218.92	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]	192.191	190.551	1.00861
2040	brachyury protein (t protein). [swissprot;acc:o15178]	208.803	210.586	1.00854
2041	ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131]	195.141	196.808
2042	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	208.803	210.586
2043	ubiquilin 1 isoform 1. [refseq;acc:nm_013438]	195.173	196.837	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]	198.24	199.928	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]	226.003	224.124	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]	222.634	220.787	1.00837
2050	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	216.981	218.79	1.00834
2051	oxidation resistance 1. [refseq;acc:nm_181354]
2052	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	205.95	207.667
2053	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]	216.981	218.79
2054	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	205.948	207.665
2055	dymeclin. [refseq;acc:nm_017653]	216.981	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	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	205.923	207.638	1.00833
2064	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	205.939	207.655
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]	212.561	214.328	1.00831
2066	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	231.001	229.102	1.00829
2067	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566]	191.639	193.226	1.00828
2068	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	222.61	220.8	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]	215.807	217.555	1.0081
2070	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	225.008	223.199
2071	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	215.807	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	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	227.433	229.267	1.00806
2074	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098]	214.599	216.324	1.00804

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.