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

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Showing element 900 to 949 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
900	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]	229.171	238.048	1.03874
901	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945]	237.62	228.762	1.03872
902	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
903	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821]	246.354	237.223	1.03849
904	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]
905	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	230.768	239.632	1.03841
906	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	230.764	239.62	1.03838
907	junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923]	223.906	215.653	1.03827
908	tax interaction protein 1. [refseq;acc:nm_014604]
909	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	142.077	136.846	1.03823
910	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	217.168	209.207	1.03805
911	ero1-like. [refseq;acc:nm_014584]
912	wd-repeat protein 3. [swissprot;acc:q9unx4]	243.896	234.96	1.03803
913	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	210.863	218.878	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. [refseq;acc:nm_020399]
915	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	146.036	140.692	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). [swissprot;acc:q9nyq3]	232.512	241.288	1.03774
917	parafibromin. [refseq;acc:nm_024529]	239.704	230.991	1.03772
918	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	212.952	205.292	1.03731
919	midasin (midas-containing protein). [swissprot;acc:q9nu22]	237.218	228.698	1.03725
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]	236.741	245.547	1.0372
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]	215.665	207.942	1.03714
926	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [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). [swissprot;acc:p21378]
928	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	225.976	218.017	1.03651
929	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	225.955	218.015	1.03642
930	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	231.357	239.778	1.0364
931	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	159.13	164.917	1.03637
932	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	225.939	218.013	1.03636
933	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	159.165	164.951	1.03635
934	nucleolar rna-associated protein alpha isoform. [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). [refseq;acc:nm_016538]	232.473	224.372	1.03611
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]	220.246	212.618	1.03588
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]	216.501	224.27
940	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	212.442	205.088	1.03586
941	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	212.437	205.083
942	grancalcin. [swissprot;acc:p28676]	212.442	205.088
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]	212.437	205.083
945	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	212.44	205.085
946	histone h4. [swissprot;acc:p02304]	227.765	219.902	1.03576
947	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	212.51	205.191	1.03567
948	target of myb protein 1. [swissprot;acc:o60784]	217.254	209.824	1.03541
949	huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229]	217.253	209.826	1.0354

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.