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 875 to 924 of 3228 in total

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

Rank	description	red	green	network_comparison
875	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	212.002	203.954	1.03946
876	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]
877	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]
878	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]
879	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]
880	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]
881	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	227.604	219.001	1.03928
882	n-myc proto-oncogene protein. [swissprot;acc:p04198]	227.601	219.008	1.03924
883	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	227.596	219.017	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	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]		219.018
887	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	244.155	234.96	1.03913
888	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	212.027	204.05	1.03909
889	alpha-nac protein. [sptrembl;acc:q9h009]	212.028	204.053	1.03908
890	syntaxin 7. [swissprot;acc:o15400]	217.181	209.012
891	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	212.028	204.055	1.03907
892	di-ras2. [refseq;acc:nm_017594]
893	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	227.585	219.037	1.03903
894	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	217.491	209.323	1.03902
895	phenylalanine-trna synthetase. [refseq;acc:nm_006567]
896	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	230.811	239.785	1.03888
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	272.878	283.472	1.03882
898	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	229.171	238.048	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	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]

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.