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 2601 to 2650 of 3228 in total

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

Rank	description	red	green	network_comparison
2601	cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623]	214.502	214.2	1.00141
2602	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	224.875	225.192
2603	cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184]	214.494	214.192
2604	cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649]	214.486	214.184
2605	tcd37 homolog; prune. [refseq;acc:nm_021222]	214.495	214.193
2606	cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348]	214.5	214.198
2607	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	215.497	215.799	1.0014
2608	nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]
2609	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]
2610	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826]
2611	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]
2612	proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721]
2613	adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]
2614	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	202.821	202.54	1.00139
2615	transcription factor relb (i-rel). [swissprot;acc:q01201]
2616	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]
2617	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
2618	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	190.166	190.429	1.00138
2619	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	220.024	219.722	1.00137
2620	26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	215.615	215.91
2621	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	224.891	225.195	1.00135
2622	zinc finger protein 258. [refseq;acc:nm_145310]
2623	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]
2624	zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]
2625	wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	204.304	204.028
2626	actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]	224.891	225.195
2627	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]
2628	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]
2629	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
2630	zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]
2631	actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
2632	arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]
2633	nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]
2634	actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]
2635	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	166.612	166.393	1.00132
2636	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	195.635	195.384	1.00128
2637	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	187.075	186.84	1.00126
2638	junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624]	204.911	205.168	1.00125
2639	myosin viia. [swissprot;acc:q13402]	220.658	220.386	1.00123
2640	ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567]
2641	ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459]
2642	topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027]	194.097	194.328	1.00119
2643	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
2644	atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]
2645	probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]
2646	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8]	213.169	213.417	1.00116
2647	s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266]	212.496	212.25
2648	sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676]	213.169	213.417
2649	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	213.63	213.874	1.00114
2650	kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685]	217.188	216.942	1.00113

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.