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 Value Type description Network Comparison Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 725 to 774 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	network_comparison	green	
725	mevalonate kinase (ec 2.7.1.36) (mk). [source:swissprot;acc:q03426]	235.296	1.0526	247.673	
726	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	244.495	1.05196	232.419	
727	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [source:swissprot;acc:o60285]	208.873	1.05188	219.71	
728	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [source:swissprot;acc:o43505]	208.874	1.05187	219.708	
729	huntingtin interacting protein e; huntingtin interactor protein e. [source:refseq;acc:nm_007076]	208.874	1.05187	219.708	
730	mitochondrial import inner membrane translocase subunit tim10. [source:swissprot;acc:q9y5j8]	208.874	1.05187	219.708	
731	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [source:swissprot;acc:p07954]	208.874	1.05187	219.708	
732	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	124.434	1.05169	118.318	
733	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	164	1.05154	155.961	
734	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [source:swissprot;acc:q8tct8]	232.601	1.0513	244.534	
735	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [source:swissprot;acc:p17080]	232.601	1.0513	244.534	
736	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	232.601	1.0513	244.534	
737	septin 10 isoform 1. [source:refseq;acc:nm_144710]	125.526	1.05129	119.402	
738	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	222.825	1.05123	211.966	
739	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [source:swissprot;acc:o15067]	223.58	1.0512	235.027	
740	bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [source:swissprot;acc:p31939]	223.58	1.0512	235.027	
741	multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [source:swissprot;acc:p22234]	223.58	1.0512	235.027	
742	brain protein 44. [source:swissprot;acc:o95563]	126.215	1.05111	120.078	
743	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	126.215	1.05111	120.078	
744	septin 6. [source:swissprot;acc:q14141]	126.604	1.05098	120.463	
745	solute carrier family 35, member b1; udp-galactose transporter related. [source:refseq;acc:nm_005827]	214.679	1.05072	225.568	
746	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	250.465	1.0507	238.38	
747	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	250.465	1.0507	238.38	
748	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	245.246	1.05038	233.483	
749	exocyst complex component sec15b. [source:swissprot;acc:q9y2d4]	221.968	1.05036	211.326	
750	exocyst complex component sec15a. [source:swissprot;acc:q8tag9]	222.138	1.05028	211.503	
751	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	223.463	1.04974	212.875	
752	step ii splicing factor slu7. [source:refseq;acc:nm_006425]	223.463	1.04974	212.875	
753	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	224.434	1.04968	235.583	
754	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [source:swissprot;acc:q15005]	224.434	1.04968	235.583	
755	uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [source:swissprot;acc:p11172]	224.434	1.04968	235.583	
756	cleft lip and palate associated transmembrane protein 1. [source:refseq;acc:nm_001294]	224.434	1.04968	235.583	
757	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [source:swissprot;acc:p17213]	224.434	1.04968	235.583	
758	phospholipid transfer protein precursor (lipid transfer protein ii). [source:swissprot;acc:p55058]	224.434	1.04968	235.583	
759	osteoclast stimulating factor 1. [source:swissprot;acc:q92882]	231.809	1.04952	243.289	
760	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	246.055	1.04946	234.458	
761	signal transduction protein cbl-b (sh3-binding protein cbl-b). [source:swissprot;acc:q13191]	213.325	1.0493	203.303	
762	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [source:swissprot;acc:p22681]	213.256	1.0493	203.237	
763	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [source:swissprot;acc:q9y5n5]	228.78	1.04901	218.091	
764	u4/u6-associated rna splicing factor. [source:refseq;acc:nm_004698]	222.082	1.04901	211.707	
765	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [source:swissprot;acc:q9y5r4]	229.045	1.04901	218.343	
766	protein tara (trio-associated repeat on actin) (hrihfb2122). [source:swissprot;acc:q9h2d6]	213.804	1.04875	224.226	
767	rho interacting protein 3. [source:refseq;acc:nm_015134]	213.803	1.04874	224.224	
768	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [source:swissprot;acc:q9udy4]	210.946	1.04873	221.225	
769	cab2. [source:refseq;acc:nm_033419]	210.946	1.04873	221.225	
770	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [source:swissprot;acc:o75953]	210.946	1.04873	221.225	
771	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [source:swissprot;acc:p25685]	210.946	1.04873	221.225	
772	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [source:swissprot;acc:p46055]	210.946	1.04873	221.225	
773	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [source:refseq;acc:nm_022553]	210.946	1.04873	221.225	
774	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [source:refseq;acc:nm_139279]	225.996	1.04854	215.535	

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/