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 Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 908 to 957 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
908	tax interaction protein 1. [source:refseq;acc:nm_014604]	215.653	223.906	1.03827	
909	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	136.846	142.077	1.03823	
910	uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	209.207	217.168	1.03805	
911	ero1-like. [source:refseq;acc:nm_014584]	209.207	217.168	1.03805	
912	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	234.96	243.896	1.03803	
913	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source:refseq;acc:nm_024831]	218.878	210.863	1.03801	
914	pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [source:refseq;acc:nm_020399]	218.878	210.863	1.03801	
915	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	140.692	146.036	1.03798	
916	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [source:swissprot;acc:q9nyq3]	241.288	232.512	1.03774	
917	parafibromin. [source:refseq;acc:nm_024529]	230.991	239.704	1.03772	
918	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	205.292	212.952	1.03731	
919	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	228.698	237.218	1.03725	
920	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [source:swissprot;acc:o75398]	245.547	236.741	1.0372	
921	rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	245.547	236.741	1.0372	
922	map/microtubule affinity-regulating kinase 1. [source:refseq;acc:nm_018650]	245.547	236.741	1.0372	
923	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [source:refseq;acc:nm_004954]	245.547	236.741	1.0372	
924	meiotic recombination protein spo11. [source:swissprot;acc:q9y5k1]	245.547	236.741	1.0372	
925	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	207.942	215.665	1.03714	
926	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	210.139	217.942	1.03713	
927	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	210.139	217.942	1.03713	
928	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	218.017	225.976	1.03651	
929	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [source:swissprot;acc:o75352]	218.015	225.955	1.03642	
930	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [source:swissprot;acc:p14618]	239.778	231.357	1.0364	
931	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	164.917	159.13	1.03637	
932	mitochondrial translational release factor 1-like. [source:refseq;acc:nm_019041]	218.013	225.939	1.03636	
933	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [source:refseq;acc:nm_152414]	164.951	159.165	1.03635	
934	nucleolar rna-associated protein alpha isoform. [source:refseq;acc:nm_022917]	233.544	242.024	1.03631	
935	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	224.372	232.473	1.03611	
936	casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [source:swissprot;acc:p13862]	224.372	232.473	1.03611	
937	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	212.618	220.246	1.03588	
938	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	212.618	220.246	1.03588	
939	breast cancer type 1 susceptibility protein. [source:swissprot;acc:p38398]	224.27	216.501	1.03588	
940	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [source:swissprot;acc:p04632]	205.088	212.442	1.03586	
941	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [source:swissprot;acc:o14497]	205.083	212.437	1.03586	
942	grancalcin. [source:swissprot;acc:p28676]	205.088	212.442	1.03586	
943	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	205.087	212.442	1.03586	
944	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [source:swissprot;acc:o75340]	205.083	212.437	1.03586	
945	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [source:refseq;acc:nm_020732]	205.085	212.44	1.03586	
946	histone h4. [source:swissprot;acc:p02304]	219.902	227.765	1.03576	
947	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	205.191	212.51	1.03567	
948	target of myb protein 1. [source:swissprot;acc:o60784]	209.824	217.254	1.03541	
949	huntingtin-associated protein-interacting protein (duo protein). [source:swissprot;acc:o60229]	209.826	217.253	1.0354	
950	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [source:swissprot;acc:p28715]	261.821	252.873	1.03539	
951	triple functional domain protein (ptprf interacting protein). [source:swissprot;acc:o75962]	209.827	217.253	1.03539	
952	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [source:refseq;acc:nm_144678]	209.83	217.252	1.03537	
953	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [source:swissprot;acc:q01780]	205.466	198.494	1.03512	
954	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [source:swissprot;acc:o43708]	276.773	267.447	1.03487	
955	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [source:swissprot;acc:q9p0m9]	239.205	231.163	1.03479	
956	vinexin (sh3-containing adaptor molecule-1) (scam-1). [source:swissprot;acc:o60504]	204.732	211.812	1.03458	
957	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	134.399	129.913	1.03453	

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/