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 733 to 782 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
733	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	164	155.961	1.05154	
734	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [source:swissprot;acc:q8tct8]	232.601	244.534	1.0513	
735	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [source:swissprot;acc:p17080]	232.601	244.534	1.0513	
736	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	232.601	244.534	1.0513	
737	septin 10 isoform 1. [source:refseq;acc:nm_144710]	125.526	119.402	1.05129	
738	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	222.825	211.966	1.05123	
739	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [source:swissprot;acc:o15067]	223.58	235.027	1.0512	
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	235.027	1.0512	
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	235.027	1.0512	
742	brain protein 44. [source:swissprot;acc:o95563]	126.215	120.078	1.05111	
743	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	126.215	120.078	1.05111	
744	septin 6. [source:swissprot;acc:q14141]	126.604	120.463	1.05098	
745	solute carrier family 35, member b1; udp-galactose transporter related. [source:refseq;acc:nm_005827]	214.679	225.568	1.05072	
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	238.38	1.0507	
747	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	250.465	238.38	1.0507	
748	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	245.246	233.483	1.05038	
749	exocyst complex component sec15b. [source:swissprot;acc:q9y2d4]	221.968	211.326	1.05036	
750	exocyst complex component sec15a. [source:swissprot;acc:q8tag9]	222.138	211.503	1.05028	
751	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	223.463	212.875	1.04974	
752	step ii splicing factor slu7. [source:refseq;acc:nm_006425]	223.463	212.875	1.04974	
753	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	224.434	235.583	1.04968	
754	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [source:swissprot;acc:q15005]	224.434	235.583	1.04968	
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	235.583	1.04968	
756	cleft lip and palate associated transmembrane protein 1. [source:refseq;acc:nm_001294]	224.434	235.583	1.04968	
757	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [source:swissprot;acc:p17213]	224.434	235.583	1.04968	
758	phospholipid transfer protein precursor (lipid transfer protein ii). [source:swissprot;acc:p55058]	224.434	235.583	1.04968	
759	osteoclast stimulating factor 1. [source:swissprot;acc:q92882]	231.809	243.289	1.04952	
760	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	246.055	234.458	1.04946	
761	signal transduction protein cbl-b (sh3-binding protein cbl-b). [source:swissprot;acc:q13191]	213.325	203.303	1.0493	
762	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [source:swissprot;acc:p22681]	213.256	203.237	1.0493	
763	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [source:swissprot;acc:q9y5n5]	228.78	218.091	1.04901	
764	u4/u6-associated rna splicing factor. [source:refseq;acc:nm_004698]	222.082	211.707	1.04901	
765	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [source:swissprot;acc:q9y5r4]	229.045	218.343	1.04901	
766	protein tara (trio-associated repeat on actin) (hrihfb2122). [source:swissprot;acc:q9h2d6]	213.804	224.226	1.04875	
767	rho interacting protein 3. [source:refseq;acc:nm_015134]	213.803	224.224	1.04874	
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	221.225	1.04873	
769	cab2. [source:refseq;acc:nm_033419]	210.946	221.225	1.04873	
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	221.225	1.04873	
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	221.225	1.04873	
772	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [source:swissprot;acc:p46055]	210.946	221.225	1.04873	
773	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [source:refseq;acc:nm_022553]	210.946	221.225	1.04873	
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	215.535	1.04854	
775	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	226.003	215.541	1.04854	
776	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [source:sptrembl;acc:q9ujn8]	225.996	215.535	1.04854	
777	histone deacetylase 1 (hd1). [source:swissprot;acc:q13547]	225.989	215.53	1.04853	
778	sorting nexin 6 (traf4-associated factor 2). [source:swissprot;acc:q9unh7]	209.191	219.332	1.04848	
779	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [source:swissprot;acc:p32321]	230.516	241.641	1.04826	
780	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [source:swissprot;acc:p41584]	232.762	243.933	1.04799	
781	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [source:refseq;acc:nm_016183]	245.84	257.636	1.04798	
782	translin. [source:swissprot;acc:q15631]	224.385	235.131	1.04789	

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/