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 Network Comparison Type Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 868 to 917 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	red	network_comparison	green	
868	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [source:swissprot;acc:p53602]	233.298	1.03975	242.571	
869	exocyst complex component sec8. [source:swissprot;acc:q96a65]	217.762	1.03969	209.449	
870	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	211.908	1.03962	203.832	
871	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	110.2	1.03949	114.552	
872	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [source:swissprot;acc:q07244]	224.413	1.03948	233.272	
873	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [source:swissprot;acc:o43172]	224.413	1.03948	233.272	
874	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	212.002	1.03946	203.954	
875	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [source:swissprot;acc:p54646]	212.002	1.03946	203.954	
876	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [source:swissprot;acc:q13131]	212.002	1.03946	203.954	
877	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	212.002	1.03946	203.954	
878	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	212.002	1.03946	203.954	
879	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	212.002	1.03946	203.954	
880	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	212.002	1.03946	203.954	
881	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	227.604	1.03928	219.001	
882	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	227.601	1.03924	219.008	
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	1.03917	219.017	
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	1.03917	219.017	
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	1.03917	219.017	
886	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	227.596	1.03917	219.018	
887	transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	244.155	1.03913	234.96	
888	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	212.027	1.03909	204.05	
889	alpha-nac protein. [source:sptrembl;acc:q9h009]	212.028	1.03908	204.053	
890	syntaxin 7. [source:swissprot;acc:o15400]	217.181	1.03908	209.012	
891	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	212.028	1.03907	204.055	
892	di-ras2. [source:refseq;acc:nm_017594]	212.028	1.03907	204.055	
893	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	227.585	1.03903	219.037	
894	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [source:swissprot;acc:q9y285]	217.491	1.03902	209.323	
895	phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	217.491	1.03902	209.323	
896	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [source:swissprot;acc:p52435]	230.811	1.03888	239.785	
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [source:swissprot;acc:o15530]	272.878	1.03882	283.472	
898	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	229.171	1.03874	238.048	
899	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [source:refseq;acc:nm_032243]	229.171	1.03874	238.048	
900	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [source:swissprot;acc:p10599]	229.171	1.03874	238.048	
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	1.03872	228.762	
902	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	237.62	1.03872	228.762	
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	1.03849	237.223	
904	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	246.354	1.03849	237.223	
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	1.03841	239.632	
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	1.03838	239.62	
907	junction plakoglobin (desmoplakin iii). [source:swissprot;acc:p14923]	223.906	1.03827	215.653	
908	tax interaction protein 1. [source:refseq;acc:nm_014604]	223.906	1.03827	215.653	
909	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	142.077	1.03823	136.846	
910	uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	217.168	1.03805	209.207	
911	ero1-like. [source:refseq;acc:nm_014584]	217.168	1.03805	209.207	
912	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	243.896	1.03803	234.96	
913	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source:refseq;acc:nm_024831]	210.863	1.03801	218.878	
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	1.03801	218.878	
915	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	146.036	1.03798	140.692	
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	1.03774	241.288	
917	parafibromin. [source:refseq;acc:nm_024529]	239.704	1.03772	230.991	

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/