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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 1777 to 1826 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
889	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [source:swissprot;acc:q13131]	Subtracted	212.002	203.954	8.048	
889	alpha-nac protein. [source:sptrembl;acc:q9h009]	Divided	212.028	204.053	1.03908	
890	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	Subtracted	212.002	203.954	8.048	
890	syntaxin 7. [source:swissprot;acc:o15400]	Divided	217.181	209.012	1.03908	
891	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	Subtracted	212.002	203.954	8.048	
891	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	Divided	212.028	204.055	1.03907	
892	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	Subtracted	212.002	203.954	8.048	
892	di-ras2. [source:refseq;acc:nm_017594]	Divided	212.028	204.055	1.03907	
893	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	Subtracted	212.002	203.954	8.048	
893	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	Divided	227.585	219.037	1.03903	
894	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [source:swissprot;acc:q9p0m9]	Subtracted	231.163	239.205	8.042	
894	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [source:swissprot;acc:q9y285]	Divided	217.491	209.323	1.03902	
895	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Subtracted	164	155.961	8.039	
895	phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	Divided	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]	Divided	230.811	239.785	1.03888	
896	t-cell activation wd repeat protein. [source:refseq;acc:nm_139281]	Subtracted	243.34	235.322	8.018	
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [source:swissprot;acc:o15530]	Divided	272.878	283.472	1.03882	
897	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source:refseq;acc:nm_024831]	Subtracted	210.863	218.878	8.015	
898	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Divided	229.171	238.048	1.03874	
898	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]	Subtracted	210.863	218.878	8.015	
899	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	Subtracted	212.027	204.05	7.977	
899	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [source:refseq;acc:nm_032243]	Divided	229.171	238.048	1.03874	
900	alpha-nac protein. [source:sptrembl;acc:q9h009]	Subtracted	212.028	204.053	7.975	
900	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [source:swissprot;acc:p10599]	Divided	229.171	238.048	1.03874	
901	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	Subtracted	212.028	204.055	7.973	
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]	Divided	237.62	228.762	1.03872	
902	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	Divided	237.62	228.762	1.03872	
902	di-ras2. [source:refseq;acc:nm_017594]	Subtracted	212.028	204.055	7.973	
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]	Divided	246.354	237.223	1.03849	
903	uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	Subtracted	217.168	209.207	7.961	
904	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	Subtracted	243.312	235.351	7.961	
904	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	Divided	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]	Divided	230.768	239.632	1.03841	
905	ero1-like. [source:refseq;acc:nm_014584]	Subtracted	217.168	209.207	7.961	
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]	Divided	230.764	239.62	1.03838	
906	pbk1 protein. [source:sptrembl;acc:o76021]	Subtracted	243.312	235.353	7.959	
907	junction plakoglobin (desmoplakin iii). [source:swissprot;acc:p14923]	Divided	223.906	215.653	1.03827	
907	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	Subtracted	225.976	218.017	7.959	
908	sedlin. [source:swissprot;acc:o14582]	Subtracted	129.219	121.261	7.958	
908	tax interaction protein 1. [source:refseq;acc:nm_014604]	Divided	223.906	215.653	1.03827	
909	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Divided	142.077	136.846	1.03823	
909	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Subtracted	129.219	121.261	7.958	
910	bet3 homolog. [source:swissprot;acc:o43617]	Subtracted	129.219	121.261	7.958	
910	uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	Divided	217.168	209.207	1.03805	
911	ero1-like. [source:refseq;acc:nm_014584]	Divided	217.168	209.207	1.03805	
911	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [source:swissprot;acc:o75352]	Subtracted	225.955	218.015	7.94	
912	mitochondrial translational release factor 1-like. [source:refseq;acc:nm_019041]	Subtracted	225.939	218.013	7.926	
912	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	Divided	243.896	234.96	1.03803	
913	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	Subtracted	243.297	235.373	7.924	
913	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source:refseq;acc:nm_024831]	Divided	210.863	218.878	1.03801	

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/