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 1800 to 1849 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
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	
914	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [source:swissprot;acc:p25388]	Subtracted	237.558	229.677	7.881	
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]	Divided	210.863	218.878	1.03801	
915	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Divided	146.036	140.692	1.03798	
915	zuotin related factor-1 (m-phase phosphoprotein 11). [source:swissprot;acc:q99543]	Subtracted	237.558	229.677	7.881	
916	histone h4. [source:swissprot;acc:p02304]	Subtracted	227.765	219.902	7.863	
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]	Divided	232.512	241.288	1.03774	
917	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Subtracted	86.7483	78.8995	7.8488	
917	parafibromin. [source:refseq;acc:nm_024529]	Divided	239.704	230.991	1.03772	
918	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	Subtracted	217.942	210.139	7.803	
918	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	Divided	212.952	205.292	1.03731	
919	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	Subtracted	217.942	210.139	7.803	
919	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	Divided	237.218	228.698	1.03725	
920	breast cancer type 1 susceptibility protein. [source:swissprot;acc:p38398]	Subtracted	216.501	224.27	7.769	
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]	Divided	236.741	245.547	1.0372	
921	rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	Divided	236.741	245.547	1.0372	
921	wd-repeat protein bing4. [source:swissprot;acc:o15213]	Subtracted	243.227	235.475	7.752	
922	map/microtubule affinity-regulating kinase 1. [source:refseq;acc:nm_018650]	Divided	236.741	245.547	1.0372	
922	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	Subtracted	215.665	207.942	7.723	
923	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	Subtracted	193.114	185.412	7.702	
923	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [source:refseq;acc:nm_004954]	Divided	236.741	245.547	1.0372	
924	meiotic recombination protein spo11. [source:swissprot;acc:q9y5k1]	Divided	236.741	245.547	1.0372	
924	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	Subtracted	238.725	231.059	7.666	
925	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	Divided	215.665	207.942	1.03714	

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/