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 2263 to 2312 of 3228 in total

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

Rank	description	red	green	network_comparison
2263	40s ribosomal protein s3a. [swissprot;acc:p49241]	4918.64	5145.39	1.0461
2264	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	3633.74	3473.68	1.04608
2265	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	3612.45	3453.39	1.04606
2266	transcription factor iib. [refseq;acc:nm_013242]	9146.11	8743.98	1.04599
2267	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]
2268	eyes absent homolog 1. [swissprot;acc:q99502]	5785.08	6051.03	1.04597
2269	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853]	6373.94	6666.87	1.04596
2270	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	6568.41	6869.9	1.0459
2271	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	6568.51	6869.97	1.04589
2272	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
2273	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	6374.64	6667.06	1.04587
2274	eyes absent homolog 3. [swissprot;acc:q99504]	5779.66	6044.78
2275	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544]	6570.74	6872.1	1.04586
2276	sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467]	5783.69	6048.87	1.04585
2277	sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9]	5783.72	6048.9
2278	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]	5783.76	6048.94
2279	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818]	5783.73	6048.91
2280	rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156]
2281	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]
2282	adaptor-associated kinase 1. [refseq;acc:nm_014911]
2283	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]	5783.7	6048.88
2284	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	5783.73	6048.91
2285	rho-gtpase activating protein 10. [refseq;acc:nm_020824]
2286	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2]	5783.76	6048.94
2287	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	5783.7	6048.88
2288	2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953]	5783.76	6048.94
2289	ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316]
2290	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492]	5783.75	6048.93
2291	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641]	5783.71	6048.89
2292	membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835]	5783.76	6048.94
2293	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]
2294	growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861]	5783.73	6048.91
2295	glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211]	6066.61	6344.65	1.04583
2296	eyes absent homolog 4. [swissprot;acc:o95677]	5784.9	6049.99	1.04582
2297	rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094]	6570.31	6871.29	1.04581
2298	rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407]	6570.74	6871.6	1.04579
2299	eyes absent homolog 2. [swissprot;acc:o00167]	5786.15	6050.71	1.04572
2300	rh type c glycoprotein. [refseq;acc:nm_016321]	6573.3	6873.48	1.04567
2301	hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868]	6946.6	7263.68	1.04565
2302	3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035]
2303	hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581]
2304	acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752]	6946.38	7263.48
2305	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	6946.82	7263.87	1.04564
2306	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	3619.07	3461.21	1.04561
2307	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	5666.91	5923.48	1.04528
2308	60s ribosomal protein l7. [swissprot;acc:p18124]	3976.92	3804.85	1.04522
2309	delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062]	6960.96	7273.7	1.04493
2310	lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]
2311	solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330]	6961.19	7273.93
2312	very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975]	6960.26	7273.01

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.