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	network_comparison	green

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Showing element 2513 to 2562 of 3228 in total

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

Rank	description	red	network_comparison	green
2513	reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799]	6204.25	1.02521	6360.69
2514	eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9]	6203.92	1.0252	6360.25
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	1.02519	6360.24
2517	eh-domain containing protein 2. [swissprot;acc:q9nzn4]	6203.96
2518	sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422]	6204.15	1.02516	6360.27
2519	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	5964.17	1.02511	6113.96
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	1.02508	3710.01
2524	myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368]	8695.15	1.02505	8912.98
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	1.02487	6359.44
2529	protein cgi-147. [swissprot;acc:q9y3e5]	6436.43	1.02442	6283
2530	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	3880.5	1.02431	3788.42
2531	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780]	6141.97	1.02428	6291.08
2532	60s ribosomal protein l15. [swissprot;acc:p39030]	4888.72	1.02401	5006.1
2533	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	3847.84	1.02356	3759.28
2534	thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669]	6452.33	1.0235	6603.94
2535	dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]
2536	sorting nexin 1. [swissprot;acc:q13596]	5932.05	1.02348	6071.35
2537	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	6669.22	1.02327	6824.41
2538	estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659]	7121.07	1.02325	7286.61
2539	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	3805.17	1.02321	3718.86
2540	pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559]	6672.69	1.0232	6827.51
2541	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	8542.13	1.02319	8740.23
2542	osteoclast stimulating factor 1. [swissprot;acc:q92882]	4708.98	1.02302	4817.39
2543	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	8565.3	1.02277	8760.3
2544	peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044]	6239.69	1.02222	6378.35
2545	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	8285.65	1.02197	8107.49
2546	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954]	4763.99		4868.66
2547	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	3370.46	1.02187	3444.18
2548	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	4725.79	1.02087	4824.4
2549	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]
2550	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
2551	sorting nexin 17. [swissprot;acc:q15036]
2552	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	4884.35	1.02077	4985.78
2553	ras-related protein rab-37. [swissprot;acc:q96ax2]	3852.99	1.02043	3775.86
2554	ras-related protein rab-26. [swissprot;acc:q9ulw5]
2555	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
2556	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	4883.73	1.0203	4982.88
2557	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	5291.65	1.02002	5187.78
2558	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
2559	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]
2560	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
2561	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]
2562	cgthba protein (-14 gene protein). [swissprot;acc:q12980]

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.