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 - 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 1775 to 1824 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
888	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	Subtracted	212.002	203.954	8.048
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Divided	212.027	204.05	1.03909
889	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	Subtracted	212.002	203.954	8.048
	alpha-nac protein. [sptrembl;acc:q9h009]	Divided	212.028	204.053	1.03908
890	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	Subtracted	212.002	203.954	8.048
	syntaxin 7. [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). [swissprot;acc:q9ugi9]	Subtracted	212.002	203.954	8.048
	small gtp-binding tumor suppressor 1. [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). [swissprot;acc:q9y478]	Subtracted	212.002	203.954	8.048
	di-ras2. [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). [swissprot;acc:q9ugj0]	Subtracted	212.002	203.954	8.048
	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	Divided	227.585	219.037	1.03903
894	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9]	Subtracted	231.163	239.205	8.042
	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [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). [swissprot;acc:p49748]	Subtracted	164	155.961	8.039
	phenylalanine-trna synthetase. [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). [swissprot;acc:p52435]		230.811	239.785	1.03888
	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	Subtracted	243.34	235.322	8.018
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	Divided	272.878	283.472	1.03882
	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	Subtracted	210.863	218.878	8.015
898	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Divided	229.171	238.048	1.03874
	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]	Subtracted	210.863	218.878	8.015
899	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]		212.027	204.05	7.977
	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]	Divided	229.171	238.048	1.03874
900	alpha-nac protein. [sptrembl;acc:q9h009]	Subtracted	212.028	204.053	7.975
	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]	Divided	229.171	238.048	1.03874
901	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	Subtracted	212.028	204.055	7.973
	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]	Divided	237.62	228.762	1.03872
902	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
	di-ras2. [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). [swissprot;acc:o75821]	Divided	246.354	237.223	1.03849
	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	Subtracted	217.168	209.207	7.961
904	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]		243.312	235.351
	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [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. [refseq;acc:nm_032959]		230.768	239.632	1.03841
	ero1-like. [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. [refseq;acc:nm_145325]	Divided	230.764	239.62	1.03838
	pbk1 protein. [sptrembl;acc:o76021]	Subtracted	243.312	235.353	7.959
907	junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923]	Divided	223.906	215.653	1.03827
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Subtracted	225.976	218.017	7.959
908	sedlin. [swissprot;acc:o14582]		129.219	121.261	7.958
	tax interaction protein 1. [refseq;acc:nm_014604]	Divided	223.906	215.653	1.03827
909	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]		142.077	136.846	1.03823
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Subtracted	129.219	121.261	7.958
910	bet3 homolog. [swissprot;acc:o43617]
	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	Divided	217.168	209.207	1.03805
911	ero1-like. [refseq;acc:nm_014584]
	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	Subtracted	225.955	218.015	7.94
912	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]		225.939	218.013	7.926
	wd-repeat protein 3. [swissprot;acc:q9unx4]	Divided	243.896	234.96	1.03803

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.