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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 877 to 926 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
877	PRKAB2	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	212.002	203.954	1.03946	
878	PRKAG3	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	212.002	203.954	1.03946	
879	PRKAB1	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	212.002	203.954	1.03946	
880	PRKAG2	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	212.002	203.954	1.03946	
881	MYCL1	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	227.604	219.001	1.03928	
882	MYCN	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	227.601	219.008	1.03924	
883	GABPA	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	227.596	219.017	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]	227.596	219.017	1.03917	
885	NDUFS8	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]	227.596	219.017	1.03917	
886	ELOVL1	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	227.596	219.018	1.03917	
887	TBL3	transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	244.155	234.96	1.03913	
888		nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	212.027	204.05	1.03909	
889		alpha-nac protein. [source:sptrembl;acc:q9h009]	212.028	204.053	1.03908	
890	STX7	syntaxin 7. [source:swissprot;acc:o15400]	217.181	209.012	1.03908	
891	DIRAS1	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	212.028	204.055	1.03907	
892	DIRAS2	di-ras2. [source:refseq;acc:nm_017594]	212.028	204.055	1.03907	
893	MYC	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	227.585	219.037	1.03903	
894	FARSA	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [source:swissprot;acc:q9y285]	217.491	209.323	1.03902	
895	FARS2	phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	217.491	209.323	1.03902	
896	POLR2J	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [source:swissprot;acc:p52435]	230.811	239.785	1.03888	
897	PDPK1	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [source:swissprot;acc:o15530]	272.878	283.472	1.03882	
898		60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	229.171	238.048	1.03874	
899	TXNDC2	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [source:refseq;acc:nm_032243]	229.171	238.048	1.03874	
900	TXN	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [source:swissprot;acc:p10599]	229.171	238.048	1.03874	
901	SSRP1	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]	237.62	228.762	1.03872	
902	SUPT16H	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	237.62	228.762	1.03872	
903	EIF3G	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [source:swissprot;acc:o75821]	246.354	237.223	1.03849	
904	EIF3A	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	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]	230.768	239.632	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]	230.764	239.62	1.03838	
907	JUP	junction plakoglobin (desmoplakin iii). [source:swissprot;acc:p14923]	223.906	215.653	1.03827	
908		tax interaction protein 1. [source:refseq;acc:nm_014604]	223.906	215.653	1.03827	
909	SEPT1	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	142.077	136.846	1.03823	
910		uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	217.168	209.207	1.03805	
911		ero1-like. [source:refseq;acc:nm_014584]	217.168	209.207	1.03805	
912	WDR3	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	243.896	234.96	1.03803	
913	TGS1	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source:refseq;acc:nm_024831]	210.863	218.878	1.03801	
914	GOPC	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]	210.863	218.878	1.03801	
915	TRMU	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	146.036	140.692	1.03798	
916	HAO2	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]	232.512	241.288	1.03774	
917	CDC73	parafibromin. [source:refseq;acc:nm_024529]	239.704	230.991	1.03772	
918	SORBS1	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	212.952	205.292	1.03731	
919	MDN1	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	237.218	228.698	1.03725	
920	DEAF1	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]	236.741	245.547	1.0372	
921	RIOK1	rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	236.741	245.547	1.0372	
922	MARK1	map/microtubule affinity-regulating kinase 1. [source:refseq;acc:nm_018650]	236.741	245.547	1.0372	
923	MARK2	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [source:refseq;acc:nm_004954]	236.741	245.547	1.0372	
924	SPO11	meiotic recombination protein spo11. [source:swissprot;acc:q9y5k1]	236.741	245.547	1.0372	
925	PEF1	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	215.665	207.942	1.03714	
926	IMMP2L	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	217.942	210.139	1.03713	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/