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 2225 to 2274 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2225	60s ribosomal protein l9. [source:swissprot;acc:p32969]	3750.99	3580.35	1.04766	
2226	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [source:swissprot;acc:p30085]	3650.78	3484.91	1.0476	
2227	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [source:swissprot;acc:q9uij7]	3650.78	3484.91	1.0476	
2228	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	3650.82	3484.97	1.04759	
2229	surfeit locus protein 5. [source:swissprot;acc:q15528]	3650.8	3484.94	1.04759	
2230	zinc finger protein 291. [source:swissprot;acc:q9by12]	3650.8	3484.94	1.04759	
2231	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	3650.8	3484.94	1.04759	
2232	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	3650.8	3484.94	1.04759	
2233	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	3614.08	3450.07	1.04754	
2234	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	3614.07	3450.07	1.04754	
2235	40s ribosomal protein s3. [source:swissprot;acc:p23396]	3674.29	3508.13	1.04736	
2236	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [source:swissprot;acc:p05023]	5902.27	6181.21	1.04726	
2237	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [source:swissprot;acc:o60911]	5902.26	6181.21	1.04726	
2238	cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [source:swissprot;acc:p07711]	5902.27	6181.21	1.04726	
2239	sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [source:swissprot;acc:p13637]	5902.27	6181.21	1.04726	
2240	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	5902.27	6181.21	1.04726	
2241	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	3670.45	3504.91	1.04723	
2242	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	3670.45	3504.91	1.04723	
2243	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	5776.96	6049.61	1.0472	
2244	gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [source:swissprot;acc:p49915]	5776.96	6049.61	1.0472	
2245	inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [source:swissprot;acc:p20839]	5776.96	6049.61	1.0472	
2246	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [source:sptrembl;acc:q9ugb5]	6209.77	6501.99	1.04706	
2247	rna-binding protein with multiple splicing (rbp-ms). [source:swissprot;acc:q93062]	5819.36	6092.93	1.04701	
2248	signal recognition particle 54 kda protein (srp54). [source:swissprot;acc:p13624]	5833.01	6106.48	1.04688	
2249	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [source:swissprot;acc:p11766]	6834.03	7153.66	1.04677	
2250	esterase d (ec 3.1.1.1). [source:swissprot;acc:p10768]	6834.03	7153.66	1.04677	
2251	serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [source:swissprot;acc:o15270]	6196.65	6486.12	1.04671	
2252	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [source:swissprot;acc:q14161]	5840.54	6113.01	1.04665	
2253	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	3629.21	3467.48	1.04664	
2254	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [source:swissprot;acc:p19652]	7383.13	7727.39	1.04663	
2255	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	3624.59	3463.37	1.04655	
2256	ubiquitin. [source:swissprot;acc:p02248]	7390.36	7733.85	1.04648	
2257	sr rich protein. [source:refseq;acc:nm_032870]	6245.32	6534.23	1.04626	
2258	60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	5150.31	5388.05	1.04616	
2259	ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [source:swissprot;acc:p56554]	6486.84	6786.23	1.04615	
2260	block 23. [source:sptrembl;acc:q8nhw5]	5150.14	5387.84	1.04615	
2261	38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [source:swissprot;acc:q14318]	6486.84	6786.23	1.04615	
2262	similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	5148.88	5386.34	1.04612	
2263	40s ribosomal protein s3a. [source:swissprot;acc:p49241]	4918.64	5145.39	1.0461	
2264	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	3633.74	3473.68	1.04608	
2265	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	3612.45	3453.39	1.04606	
2266	transcription factor iib. [source:refseq;acc:nm_013242]	9146.11	8743.98	1.04599	
2267	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [source:swissprot;acc:q12872]	9146.11	8743.98	1.04599	
2268	eyes absent homolog 1. [source: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). [source: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). [source:swissprot;acc:p18577]	6568.41	6869.9	1.0459	
2271	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [source: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). [source:swissprot;acc:p18577]	6568.51	6869.97	1.04589	
2273	upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415]	6374.64	6667.06	1.04587	
2274	eyes absent homolog 3. [source:swissprot;acc:q99504]	5779.66	6044.78	1.04587	

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/