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 962 to 1011 of 3228 in total

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

Rank	description	red	green	network_comparison	
962	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	11773	10733.2	1.09688	
963	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [source:swissprot;acc:p13073]	11773	10733.2	1.09688	
964	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [source:swissprot;acc:q96kj9]	11773	10733.2	1.09688	
965	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	11773.7	10733.8	1.09688	
966	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	7817.9	8575.12	1.09686	
967	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	7813.35	8569.96	1.09684	
968	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	7813.48	8570.11	1.09684	
969	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	7813.34	8569.95	1.09684	
970	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [source:swissprot;acc:q9y2j2]	7813.45	8570.07	1.09684	
971	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [source:swissprot;acc:o43491]	7813.36	8569.97	1.09684	
972	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [source:swissprot;acc:q9brk5]	7813.48	8570.11	1.09684	
973	galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	7810.11	8566.29	1.09682	
974	dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [source:swissprot;acc:q99518]	5365.06	5884.52	1.09682	
975	dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [source:swissprot;acc:q01740]	5365.14	5884.43	1.09679	
976	dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [source:swissprot;acc:p31512]	5365.22	5884.32	1.09675	
977	u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [source:swissprot;acc:o00566]	4115.9	4513.14	1.09651	
978	vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [source:swissprot;acc:p19065]	6654.42	7296.51	1.09649	
979	vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [source:swissprot;acc:p23763]	6654.42	7296.51	1.09649	
980	vesicule-associated membrane protein 4 (vamp-4). [source:swissprot;acc:o75379]	6654.42	7296.51	1.09649	
981	cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [source:swissprot;acc:o14735]	6654.42	7296.51	1.09649	
982	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [source:swissprot;acc:q8n6t3]	6654.42	7296.51	1.09649	
983	vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [source:swissprot;acc:q15836]	6654.42	7296.51	1.09649	
984	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [source:swissprot;acc:q9y287]	6362.64	6976.1	1.09642	
985	integral membrane protein 2c (transmembrane protein bri3) (npd018). [source:swissprot;acc:q9nqx7]	6362.64	6976.1	1.09642	
986	integral membrane protein 2a (e25 protein). [source:swissprot;acc:o43736]	6362.64	6976.1	1.09642	
987	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [source:swissprot;acc:q13368]	6660.04	7301.81	1.09636	
988	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [source:swissprot;acc:q16781]	6229.69	6829.58	1.0963	
989	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [source:refseq;acc:nm_005843]	11743.3	10712.3	1.09624	
990	dead-box protein 4 (vasa homolog). [source:swissprot;acc:q9nqi0]	5147.9	5641.25	1.09584	
991	transformer-2 protein homolog (tra-2 alpha). [source:swissprot;acc:q13595]	6472.38	7092.65	1.09583	
992	putative sialoglycoprotease type 2. [source:refseq;acc:nm_022353]	5393.37	5909.47	1.09569	
993	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [source:swissprot;acc:q15815]	6499.89	7121.77	1.09568	
994	interleukin-4 induced protein 1 precursor (fig-1 protein). [source:swissprot;acc:q96rq9]	5800.95	6355.71	1.09563	
995	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [source:swissprot;acc:p50995]	5778.65	6328.56	1.09516	
996	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [source:swissprot;acc:q96dp5]	5110.6	5596.73	1.09512	
997	nucleolar protein family a, member 2; component of the h/aca snornp. [source:refseq;acc:nm_017838]	5144.74	5634	1.0951	
998	transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [source:swissprot;acc:p35269]	5144.74	5634	1.0951	
999	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [source:swissprot;acc:p07098]	5680.76	6220.45	1.095	
1000	ba304i5.1 (novel lipase) (fragment). [source:sptrembl;acc:q96lg2]	5680.76	6220.45	1.095	
1001	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [source:swissprot;acc:p38571]	5680.76	6220.45	1.095	
1002	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [source:swissprot;acc:q9np81]	5680.76	6220.45	1.095	
1003	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [source:swissprot;acc:p49591]	5680.76	6220.45	1.095	
1004	o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	5391.64	5903.72	1.09498	
1005	annexin a7 (annexin vii) (synexin). [source:swissprot;acc:p20073]	5780.34	6329.3	1.09497	
1006	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	5707.73	6249.1	1.09485	
1007	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	5707.73	6249.1	1.09485	
1008	single-minded homolog 1. [source:swissprot;acc:p81133]	5707.73	6249.1	1.09485	
1009	synapsin iii. [source:swissprot;acc:o14994]	5791.82	6340.86	1.0948	
1010	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm_032468]	5791.82	6340.86	1.0948	
1011	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [source:swissprot;acc:q9y5j3]	5791.82	6340.86	1.0948	

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/