Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 2433 to 2482 of 3228 in total

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

Rank	description	red	green	network_comparison	
2433	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [source:swissprot;acc:p04720]	217.366	218.117	1.00346	
2434	methylenetetrahydrofolate reductase (ec 1.5.1.20). [source:swissprot;acc:p42898]	213.021	212.286	1.00346	
2435	zinc-finger protein zpr1 (zinc finger protein 259). [source:swissprot;acc:o75312]	217.366	218.117	1.00346	
2436	elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [source:swissprot;acc:q05639]	217.366	218.117	1.00346	
2437	guanylate kinase (ec 2.7.4.8) (gmp kinase). [source:swissprot;acc:q16774]	219.361	220.116	1.00344	
2438	proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [source:swissprot;acc:p25789]	214.049	213.323	1.0034	
2439	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [source:swissprot;acc:p31946]	220.681	221.425	1.00337	
2440	26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [source:swissprot;acc:o43242]	217.645	218.376	1.00336	
2441	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [source:swissprot;acc:p13804]	180.137	180.732	1.0033	
2442	transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [source:swissprot;acc:p49848]	204.419	203.748	1.00329	
2443	ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [source:swissprot;acc:p50550]	217.073	216.364	1.00328	
2444	zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [source:swissprot;acc:q9hc78]	206.086	206.753	1.00324	
2445	kruppel-related zinc finger protein hckrox. [source:refseq;acc:nm_015872]	206.088	206.756	1.00324	
2446	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	182.272	181.683	1.00324	
2447	peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [source:swissprot;acc:o00628]	206.084	206.752	1.00324	
2448	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [source:swissprot;acc:p23378]	212.446	211.766	1.00321	
2449	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). [source:swissprot;acc:o95674]	204.717	205.371	1.00319	
2450	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). [source:swissprot;acc:p28072]	213.85	213.177	1.00316	
2451	secretory carrier-associated membrane protein 2. [source:swissprot;acc:o15127]	204.688	205.333	1.00315	
2452	secretory carrier-associated membrane protein 3. [source:swissprot;acc:o14828]	204.688	205.333	1.00315	
2453	secretory carrier-associated membrane protein 1. [source:swissprot;acc:o15126]	204.688	205.332	1.00315	
2454	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [source:swissprot;acc:q9ukg4]	204.683	205.326	1.00314	
2455	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [source:swissprot;acc:q8wwt9]	204.683	205.326	1.00314	
2456	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [source:swissprot;acc:q9bzw2]	204.683	205.326	1.00314	
2457	vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [source:swissprot;acc:p46459]	213.588	212.92	1.00314	
2458	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [source:swissprot;acc:q13183]	204.683	205.326	1.00314	
2459	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	204.653	205.286	1.00309	
2460	pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]	235.812	235.088	1.00308	
2461	solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [source:refseq;acc:nm_006749]	235.812	235.088	1.00308	
2462	farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [source:swissprot;acc:p14324]	235.812	235.088	1.00308	
2463	protocadherin 15 precursor. [source:swissprot;acc:q96qu1]	235.812	235.088	1.00308	
2464	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [source:refseq;acc:nm_005415]	235.812	235.088	1.00308	
2465	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	235.812	235.088	1.00308	
2466	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [source:swissprot;acc:p08151]	235.812	235.088	1.00308	
2467	suppressor of fused. [source:refseq;acc:nm_016169]	235.812	235.088	1.00308	
2468	zinc finger protein gli3. [source:swissprot;acc:p10071]	235.812	235.088	1.00308	
2469	limb region 1 protein; limb region 1. [source:refseq;acc:nm_022458]	235.812	235.088	1.00308	
2470	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [source:swissprot;acc:p20142]	235.812	235.088	1.00308	
2471	zinc finger protein gli2 (tax helper protein). [source:swissprot;acc:p10070]	235.812	235.088	1.00308	
2472	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [source:refseq;acc:nm_022748]	218.218	217.564	1.00301	
2473	c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [source:swissprot;acc:q9upt6]	218.644	217.991	1.003	
2474	26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [source:swissprot;acc:p17980]	216.64	217.285	1.00298	
2475	c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [source:refseq;acc:nm_015319]	218.219	217.571	1.00298	
2476	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [source:refseq;acc:nm_005108]	211.205	210.577	1.00298	
2477	mitochondrial ribosomal protein l30 isoform a. [source:refseq;acc:nm_145212]	216.177	216.801	1.00289	
2478	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [source:swissprot;acc:q92524]	216.177	216.801	1.00289	
2479	rho-gtpase-activating protein 8. [source:swissprot;acc:q9nsg0]	218.093	218.72	1.00287	
2480	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [source:swissprot;acc:q07960]	218.093	218.72	1.00287	
2481	kinesin light chain 2 (klc 2). [source:swissprot;acc:q9h0b6]	218.093	218.72	1.00287	
2482	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [source:swissprot;acc:p33176]	218.093	218.72	1.00287	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/