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 2480 to 2529 of 3228 in total

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

Rank	description	red	green	network_comparison
2480	zinc finger protein 305. [swissprot;acc:o43309]	3568.95	3676.56	1.03015
2481	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	3568.8	3676.39
2482	zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771]	3568.99	3676.61
2483	zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022]	3568.8	3676.38	1.03014
2484	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	3568.45	3675.97	1.03013
2485	zinc finger protein 174 (aw-1). [swissprot;acc:q15697]	3568.18	3675.65	1.03012
2486	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	3626.38	3734.8	1.0299
2487	tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074]	6963.12	7170.02	1.02971
2488	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	5637.59	5804.47	1.0296
2489	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]
2490	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390]	6294.37	6472.9	1.02836
2491	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541]	3436.65	3531.96	1.02773
2492	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]
2493	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]
2494	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235]
2495	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]
2496	solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827]	5534.46	5684.97	1.0272
2497	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	7002.3	7192.25	1.02713
2498	helicase (fragment). [sptrembl;acc:q92771]	7002.03	7191.88	1.02711
2499	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451]	8186.02	7971.27	1.02694
2500	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	3804.53	3705.05	1.02685
2501	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	6562.71	6738.23	1.02675
2502	glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367]
2503	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597]	5996.06	6155.81	1.02664
2504	succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7]
2505	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912]	6237.83	6400.74	1.02612
2506	2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218]	6200.39	6362.25	1.0261
2507	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	4243.44	4352.56	1.02571
2508	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766]	6469.44	6634.31	1.02548
2509	reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197]	6202.78	6360.79	1.02547
2510	succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643]	6256.49	6415.21	1.02537
2511	integral membrane protein cii-3b. [sptrembl;acc:o75609]	6256.42	6415.04	1.02535
2512	reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298]	6203.05	6360.18	1.02533
2513	reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799]	6204.25	6360.69	1.02521
2514	eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9]	6203.92	6360.25	1.0252
2515	eh-domain containing protein 3. [swissprot;acc:q9nzn3]	6203.94
2516	eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223]	6203.95	6360.24	1.02519
2517	eh-domain containing protein 2. [swissprot;acc:q9nzn4]	6203.96
2518	sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422]	6204.15	6360.27	1.02516
2519	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	5964.17	6113.96	1.02511
2520	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]
2521	17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
2522	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725]
2523	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	3803.04	3710.01	1.02508
2524	myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368]	8695.15	8912.98	1.02505
2525	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]
2526	ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441]
2527	large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379]
2528	reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3]	6205.14	6359.44	1.02487
2529	protein cgi-147. [swissprot;acc:q9y3e5]	6436.43	6283	1.02442

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.