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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green 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	Hugo	description	red	green	network_comparison	
908		tax interaction protein 1. [source:refseq;acc:nm_014604]	223.906	215.653	1.03827	
909	SEPT1	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	142.077	136.846	1.03823	
910		uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	217.168	209.207	1.03805	
911		ero1-like. [source:refseq;acc:nm_014584]	217.168	209.207	1.03805	
912	WDR3	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	243.896	234.96	1.03803	
913	TGS1	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source:refseq;acc:nm_024831]	210.863	218.878	1.03801	
914	GOPC	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	218.878	1.03801	
915	TRMU	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	146.036	140.692	1.03798	
916	HAO2	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	241.288	1.03774	
917	CDC73	parafibromin. [source:refseq;acc:nm_024529]	239.704	230.991	1.03772	
918	SORBS1	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	212.952	205.292	1.03731	
919	MDN1	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	237.218	228.698	1.03725	
920	DEAF1	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	245.547	1.0372	
921	RIOK1	rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	236.741	245.547	1.0372	
922	MARK1	map/microtubule affinity-regulating kinase 1. [source:refseq;acc:nm_018650]	236.741	245.547	1.0372	
923	MARK2	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [source:refseq;acc:nm_004954]	236.741	245.547	1.0372	
924	SPO11	meiotic recombination protein spo11. [source:swissprot;acc:q9y5k1]	236.741	245.547	1.0372	
925	PEF1	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	215.665	207.942	1.03714	
926	IMMP2L	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	217.942	210.139	1.03713	
927		microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	217.942	210.139	1.03713	
928	MTRF1	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	225.976	218.017	1.03651	
929	MPDU1	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [source:swissprot;acc:o75352]	225.955	218.015	1.03642	
930	PKM2	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	239.778	1.0364	
931	BHLHB4	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	159.13	164.917	1.03637	
932	MTRF1L	mitochondrial translational release factor 1-like. [source:refseq;acc:nm_019041]	225.939	218.013	1.03636	
933	BHLHB5	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [source:refseq;acc:nm_152414]	159.165	164.951	1.03635	
934	NOL6	nucleolar rna-associated protein alpha isoform. [source:refseq;acc:nm_022917]	242.024	233.544	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]	232.473	224.372	1.03611	
936		casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [source:swissprot;acc:p13862]	232.473	224.372	1.03611	
937	SF3A3	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	220.246	212.618	1.03588	
938	SF3A1	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	220.246	212.618	1.03588	
939	BRCA1	breast cancer type 1 susceptibility protein. [source:swissprot;acc:p38398]	216.501	224.27	1.03588	
940	CAPNS1	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [source:swissprot;acc:p04632]	212.442	205.088	1.03586	
941	ARID1A	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	205.083	1.03586	
942	GCA	grancalcin. [source:swissprot;acc:p28676]	212.442	205.088	1.03586	
943	SRI	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	212.442	205.087	1.03586	
944	PDCD6	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [source:swissprot;acc:o75340]	212.437	205.083	1.03586	
945	ARID1B	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [source:refseq;acc:nm_020732]	212.44	205.085	1.03586	
946		histone h4. [source:swissprot;acc:p02304]	227.765	219.902	1.03576	
947	SORBS2	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	212.51	205.191	1.03567	
948	TOM1	target of myb protein 1. [source:swissprot;acc:o60784]	217.254	209.824	1.03541	
949		huntingtin-associated protein-interacting protein (duo protein). [source:swissprot;acc:o60229]	217.253	209.826	1.0354	
950	ERCC5	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	261.821	1.03539	
951	TRIO	triple functional domain protein (ptprf interacting protein). [source:swissprot;acc:o75962]	217.253	209.827	1.03539	
952	TOM1L2	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [source:refseq;acc:nm_144678]	217.252	209.83	1.03537	
953	EXOSC10	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	205.466	1.03512	
954	GSTZ1	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	276.773	1.03487	
955	MRPL27	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [source:swissprot;acc:q9p0m9]	231.163	239.205	1.03479	
956	SORBS3	vinexin (sh3-containing adaptor molecule-1) (scam-1). [source:swissprot;acc:o60504]	211.812	204.732	1.03458	
957	ARAF	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	129.913	134.399	1.03453	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/