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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Gene	Rank	Value Type	Network Comparison Type	green	Interaction Map	red	description	network_comparison	Filtered

Results: HTML CSV LaTeX

Showing element 868 to 917 of 3228 in total

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

Rank	green	red	description	network_comparison
868	242.571	233.298	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	1.03975
869	209.449	217.762	exocyst complex component sec8. [swissprot;acc:q96a65]	1.03969
870	203.832	211.908	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	1.03962
871	114.552	110.2	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	1.03949
872	233.272	224.413	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	1.03948
873			u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]
874	203.954	212.002	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	1.03946
875			5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]
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	219.001	227.604	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	1.03928
882	219.008	227.601	n-myc proto-oncogene protein. [swissprot;acc:p04198]	1.03924
883	219.017	227.596	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	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	219.018		elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]
887	234.96	244.155	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	1.03913
888	204.05	212.027	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	1.03909
889	204.053	212.028	alpha-nac protein. [sptrembl;acc:q9h009]	1.03908
890	209.012	217.181	syntaxin 7. [swissprot;acc:o15400]
891	204.055	212.028	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	1.03907
892			di-ras2. [refseq;acc:nm_017594]
893	219.037	227.585	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	1.03903
894	209.323	217.491	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	1.03902
895			phenylalanine-trna synthetase. [refseq;acc:nm_006567]
896	239.785	230.811	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	1.03888
897	283.472	272.878	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	1.03882
898	238.048	229.171	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	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	228.762	237.62	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]	1.03872
902			chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
903	237.223	246.354	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821]	1.03849
904			eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]
905	239.632	230.768	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]	1.03841
906	239.62	230.764	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]	1.03838
907	215.653	223.906	junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923]	1.03827
908			tax interaction protein 1. [refseq;acc:nm_014604]
909	136.846	142.077	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	1.03823
910	209.207	217.168	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	1.03805
911			ero1-like. [refseq;acc:nm_014584]
912	234.96	243.896	wd-repeat protein 3. [swissprot;acc:q9unx4]	1.03803
913	218.878	210.863	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	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	140.692	146.036	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	1.03798
916	241.288	232.512	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]	1.03774
917	230.991	239.704	parafibromin. [refseq;acc:nm_024529]	1.03772

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.