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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Interaction Map	Value Type	Gene	Rank	green	Filtered	description	Network Comparison Type	network_comparison	red

Results: HTML CSV LaTeX

Showing element 2408 to 2457 of 3228 in total

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

Rank	green	description	network_comparison	red
2408	193.706	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	1.00362	194.407
2409		lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760]
2410		lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330]
2411		mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]
2412		lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260]
2413	218.984	serpin b12. [swissprot;acc:q96p63]	1.00359	218.2
2414		megsin (tp55) (serpin b7). [swissprot;acc:o75635]
2415		hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
2416		oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055]
2417		upf0183 protein. [swissprot;acc:q9bsu1]
2418		antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
2419		translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232]
2420		squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508]
2421	209.454	apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797]		210.205
2422	218.984	oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133]		218.2
2423	221.471	histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6]	1.00358	220.682
2424	221.472	histone deacetylase 4 (hd4). [swissprot;acc:p56524]
2425		histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]
2426	211.618	mesoderm induction early response 1. [refseq;acc:nm_020948]	1.00357	212.374
2427		proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788]
2428	193.555	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	1.00355	192.871
2429		esterase d (ec 3.1.1.1). [swissprot;acc:p10768]
2430	218.644	epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333]	1.00354	217.873
2431	212.3	proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787]	1.00352	213.048
2432	216.556	26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]	1.00347	215.807
2433	218.117	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	1.00346	217.366
2434	212.286	methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]		213.021
2435	218.117	zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312]		217.366
2436		elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
2437	220.116	guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774]	1.00344	219.361
2438	213.323	proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789]	1.0034	214.049
2439	221.425	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	1.00337	220.681
2440	218.376	26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	1.00336	217.645
2441	180.732	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804]	1.0033	180.137
2442	203.748	transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848]	1.00329	204.419
2443	216.364	ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550]	1.00328	217.073
2444	206.753	zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78]	1.00324	206.086
2445	206.756	kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872]		206.088
2446	181.683	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]		182.272
2447	206.752	peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628]		206.084
2448	211.766	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	1.00321	212.446
2449	205.371	phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674]	1.00319	204.717
2450	213.177	proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072]	1.00316	213.85
2451	205.333	secretory carrier-associated membrane protein 2. [swissprot;acc:o15127]	1.00315	204.688
2452		secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]
2453	205.332	secretory carrier-associated membrane protein 1. [swissprot;acc:o15126]
2454	205.326	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4]	1.00314	204.683
2455		solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9]
2456		solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2]
2457	212.92	vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459]		213.588

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.