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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
    Results: HTML CSV LaTeX Showing element 1382 to 1431 of 3730 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	green	red	network_comparison	
880	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	203.954	212.002	1.03946	
881	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	219.001	227.604	1.03928	
882	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	219.008	227.601	1.03924	
883	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	219.017	227.596	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). [source:swissprot;acc:q06545]	219.017	227.596	1.03917	
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]	219.017	227.596	1.03917	
886	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	219.018	227.596	1.03917	
887	transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	234.96	244.155	1.03913	
888	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	204.05	212.027	1.03909	
889	alpha-nac protein. [source:sptrembl;acc:q9h009]	204.053	212.028	1.03908	
890	syntaxin 7. [source:swissprot;acc:o15400]	209.012	217.181	1.03908	
891	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	204.055	212.028	1.03907	
892	di-ras2. [source:refseq;acc:nm_017594]	204.055	212.028	1.03907	
893	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	219.037	227.585	1.03903	
894	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [source:swissprot;acc:q9y285]	209.323	217.491	1.03902	
895	phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	209.323	217.491	1.03902	
896	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [source:swissprot;acc:p52435]	239.785	230.811	1.03888	
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [source:swissprot;acc:o15530]	283.472	272.878	1.03882	
898	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	238.048	229.171	1.03874	
899	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [source:refseq;acc:nm_032243]	238.048	229.171	1.03874	
900	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [source:swissprot;acc:p10599]	238.048	229.171	1.03874	
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]	228.762	237.62	1.03872	
902	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	228.762	237.62	1.03872	
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]	237.223	246.354	1.03849	
904	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	237.223	246.354	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]	239.632	230.768	1.03841	
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]	239.62	230.764	1.03838	
907	junction plakoglobin (desmoplakin iii). [source:swissprot;acc:p14923]	215.653	223.906	1.03827	
908	tax interaction protein 1. [source:refseq;acc:nm_014604]	215.653	223.906	1.03827	
909	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	136.846	142.077	1.03823	
910	uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	209.207	217.168	1.03805	
911	ero1-like. [source:refseq;acc:nm_014584]	209.207	217.168	1.03805	
912	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	234.96	243.896	1.03803	
913	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source:refseq;acc:nm_024831]	218.878	210.863	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. [source:refseq;acc:nm_020399]	218.878	210.863	1.03801	
915	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	140.692	146.036	1.03798	
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]	241.288	232.512	1.03774	
917	parafibromin. [source:refseq;acc:nm_024529]	230.991	239.704	1.03772	
918	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	205.292	212.952	1.03731	
919	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	228.698	237.218	1.03725	
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]	245.547	236.741	1.0372	
921	rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	245.547	236.741	1.0372	
922	map/microtubule affinity-regulating kinase 1. [source:refseq;acc:nm_018650]	245.547	236.741	1.0372	
923	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [source:refseq;acc:nm_004954]	245.547	236.741	1.0372	
924	meiotic recombination protein spo11. [source:swissprot;acc:q9y5k1]	245.547	236.741	1.0372	
925	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	207.942	215.665	1.03714	
926	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	210.139	217.942	1.03713	
927	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	210.139	217.942	1.03713	
928	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	218.017	225.976	1.03651	
929	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [source:swissprot;acc:o75352]	218.015	225.955	1.03642	

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/