MK5 Microarray Data

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	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	network_comparison	red

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

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.