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

Results: HTML CSV LaTeX

Showing element 880 to 929 of 3228 in total

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

Rank	green	description	red	network_comparison
880	203.954	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	212.002	1.03946
881	219.001	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	227.604	1.03928
882	219.008	n-myc proto-oncogene protein. [swissprot;acc:p04198]	227.601	1.03924
883	219.017	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	227.596	1.03917
884		ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545]
885		nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217]
886	219.018	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]
887	234.96	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	244.155	1.03913
888	204.05	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	212.027	1.03909
889	204.053	alpha-nac protein. [sptrembl;acc:q9h009]	212.028	1.03908
890	209.012	syntaxin 7. [swissprot;acc:o15400]	217.181
891	204.055	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	212.028	1.03907
892		di-ras2. [refseq;acc:nm_017594]
893	219.037	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	227.585	1.03903
894	209.323	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	217.491	1.03902
895		phenylalanine-trna synthetase. [refseq;acc:nm_006567]
896	239.785	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	230.811	1.03888
897	283.472	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	272.878	1.03882
898	238.048	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	229.171	1.03874
899		thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]
900		thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]
901	228.762	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	1.03872
902		chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
903	237.223	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	1.03849
904		eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]
905	239.632	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	1.03841
906	239.62	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	1.03838
907	215.653	junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923]	223.906	1.03827
908		tax interaction protein 1. [refseq;acc:nm_014604]
909	136.846	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	142.077	1.03823
910	209.207	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	217.168	1.03805
911		ero1-like. [refseq;acc:nm_014584]
912	234.96	wd-repeat protein 3. [swissprot;acc:q9unx4]	243.896	1.03803
913	218.878	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	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. [refseq;acc:nm_020399]
915	140.692	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	146.036	1.03798
916	241.288	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	1.03774
917	230.991	parafibromin. [refseq;acc:nm_024529]	239.704	1.03772
918	205.292	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	212.952	1.03731
919	228.698	midasin (midas-containing protein). [swissprot;acc:q9nu22]	237.218	1.03725
920	245.547	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	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	207.942	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	215.665	1.03714
926	210.139	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	217.942	1.03713
927		microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
928	218.017	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	225.976	1.03651
929	218.015	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	225.955	1.03642

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.