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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 877 to 926 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
877	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	212.002	203.954	1.03946	
878	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	212.002	203.954	1.03946	
879	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	212.002	203.954	1.03946	
880	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	212.002	203.954	1.03946	
881	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	227.604	219.001	1.03928	
882	n-myc proto-oncogene protein. [source: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). [source: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). [source:swissprot;acc:q06545]	227.596	219.017	1.03917	
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). [source:swissprot;acc:o00217]	227.596	219.017	1.03917	
886	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	227.596	219.018	1.03917	
887	transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	244.155	234.96	1.03913	
888	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	212.027	204.05	1.03909	
889	alpha-nac protein. [source:sptrembl;acc:q9h009]	212.028	204.053	1.03908	
890	syntaxin 7. [source:swissprot;acc:o15400]	217.181	209.012	1.03908	
891	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	212.028	204.055	1.03907	
892	di-ras2. [source:refseq;acc:nm_017594]	212.028	204.055	1.03907	
893	myc proto-oncogene protein (c-myc). [source: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). [source:swissprot;acc:q9y285]	217.491	209.323	1.03902	
895	phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	217.491	209.323	1.03902	
896	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [source:swissprot;acc:p52435]	230.811	239.785	1.03888	
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [source:swissprot;acc:o15530]	272.878	283.472	1.03882	
898	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	229.171	238.048	1.03874	
899	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [source:refseq;acc:nm_032243]	229.171	238.048	1.03874	
900	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [source: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). [source:swissprot;acc:q08945]	237.62	228.762	1.03872	
902	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	237.62	228.762	1.03872	
903	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [source: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). [source:swissprot;acc:q14152]	246.354	237.223	1.03849	
905	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source: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. [source:refseq;acc:nm_145325]	230.764	239.62	1.03838	
907	junction plakoglobin (desmoplakin iii). [source:swissprot;acc:p14923]	223.906	215.653	1.03827	
908	tax interaction protein 1. [source:refseq;acc:nm_014604]	223.906	215.653	1.03827	
909	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	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	243.896	234.96	1.03803	
913	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source: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. [source:refseq;acc:nm_020399]	210.863	218.878	1.03801	
915	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source: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). [source:swissprot;acc:q9nyq3]	232.512	241.288	1.03774	
917	parafibromin. [source:refseq;acc:nm_024529]	239.704	230.991	1.03772	
918	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	212.952	205.292	1.03731	
919	midasin (midas-containing protein). [source: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). [source:swissprot;acc:o75398]	236.741	245.547	1.0372	
921	rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	236.741	245.547	1.0372	
922	map/microtubule affinity-regulating kinase 1. [source:refseq;acc:nm_018650]	236.741	245.547	1.0372	
923	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	meiotic recombination protein spo11. [source:swissprot;acc:q9y5k1]	236.741	245.547	1.0372	
925	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	215.665	207.942	1.03714	
926	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	217.942	210.139	1.03713	

Legend:
- Rank is the rank after comparing the two networks
- 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/