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

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

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/