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 1858 to 1907 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
1858	HNRPF	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [source:swissprot;acc:p52597]	217.893	215.545	1.01089	
1859	HNRPH1	heterogeneous nuclear ribonucleoprotein h (hnrnp h). [source:swissprot;acc:p31943]	217.895	215.547	1.01089	
1860	HNRPH2	heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [source:swissprot;acc:p55795]	217.895	215.547	1.01089	
1861	CYB5R2	cytochrome b5 reductase b5r.2. [source:refseq;acc:nm_016229]	210.856	213.147	1.01087	
1862	CYB5R1	cytochrome b5 reductase 1 (b5r.1). [source:refseq;acc:nm_016243]	210.856	213.147	1.01087	
1863	CYB5R3	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [source:swissprot;acc:p00387]	210.856	213.147	1.01087	
1864	PUF60	fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [source:refseq;acc:nm_014281]	203.071	200.89	1.01086	
1865	EIF2S3	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [source:swissprot;acc:p41091]	221.639	224.046	1.01086	
1866	EIF2B4	translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q9ui10]	221.725	224.133	1.01086	
1867		multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [source:swissprot;acc:q13155]	203.071	200.89	1.01086	
1868	TPD52L3	protein kinase nyd-sp25. [source:refseq;acc:nm_033516]	207.642	209.895	1.01085	
1869	LANCL2	lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [source:refseq;acc:nm_018697]	220.107	217.75	1.01082	
1870	LANCL1	lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [source:refseq;acc:nm_006055]	220.107	217.75	1.01082	
1871	CLPX	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [source:swissprot;acc:o76031]	222.819	225.228	1.01081	
1872	POLDIP2	dna polymerase delta p38 subunit. [source:refseq;acc:nm_015584]	222.819	225.228	1.01081	
1873		scratch; scratch 1. [source:refseq;acc:nm_031309]	210.55	208.305	1.01078	
1874		williams-beuren syndrome critical region protein 20 copy b. [source:refseq;acc:nm_145645]	223.862	226.271	1.01076	
1875	NSUN5	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [source:refseq;acc:nm_018044]	223.862	226.271	1.01076	
1876	NSUN5B	williams beuren syndrome chromosome region 20c isoform 1. [source:refseq;acc:nm_032158]	223.862	226.271	1.01076	
1877	NUCB1	nucleobindin 1 precursor (calnuc). [source:swissprot;acc:q02818]	212.186	214.467	1.01075	
1878	MLH1	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	212.186	214.467	1.01075	
1879	NUCB2	nucleobindin 2 precursor (dna-binding protein nefa). [source:swissprot;acc:p80303]	212.186	214.467	1.01075	
1880	CDA	cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [source:swissprot;acc:p32320]	220.852	223.225	1.01074	
1881		dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [source:sptrembl;acc:q9nq03]	210.592	208.355	1.01074	
1882	RPL28	60s ribosomal protein l28. [source:swissprot;acc:p46779]	215.896	213.61	1.0107	
1883	PFKP	6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	240.317	242.881	1.01067	
1884	OLA1	putative gtp-binding protein ptd004 (pro2455). [source:swissprot;acc:q9ntk5]	215.081	217.373	1.01066	
1885	ARG1	arginase 1 (ec 3.5.3.1) (liver-type arginase). [source:swissprot;acc:p05089]	204.44	206.615	1.01064	
1886	ARG2	arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [source:swissprot;acc:p78540]	204.512	206.682	1.01061	
1887	SARM1	sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [source:refseq;acc:nm_015077]	220.896	218.577	1.01061	
1888	ICT1	immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [source:swissprot;acc:q14197]	218.414	216.131	1.01056	
1889	RAB3IL1	rab3a interacting protein (rabin3)-like 1. [source:refseq;acc:nm_013401]	211.27	209.067	1.01054	
1890	RAB3IP	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [source:refseq;acc:nm_022456]	211.314	209.111	1.01054	
1891	MCM3	dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [source:swissprot;acc:p25205]	233.828	231.395	1.01051	
1892	KEAP1	kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [source:swissprot;acc:q14145]	233.828	231.395	1.01051	
1893	GMPPB	gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [source:refseq;acc:nm_013334]	222.842	225.17	1.01045	
1894	GMPPA	gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [source:refseq;acc:nm_013335]	222.842	225.17	1.01045	
1895	CAP2	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	215.853	213.639	1.01036	
1896	LDB2	lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [source:refseq;acc:nm_001290]	199.883	197.835	1.01035	
1897		lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	199.883	197.835	1.01035	
1898	LHX4	lim/homeobox protein lhx4. [source:swissprot;acc:q969g2]	199.881	197.833	1.01035	
1899	LHX3	lim/homeobox protein lhx3. [source:swissprot;acc:q9ubr4]	199.884	197.837	1.01035	
1900	SLC27A4	solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [source:refseq;acc:nm_005094]	191.401	193.38	1.01034	
1901	TM7SF2	delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [source:swissprot;acc:o76062]	191.411	193.39	1.01034	
1902	LBR	lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [source:swissprot;acc:q14739]	191.411	193.39	1.01034	
1903	SLC27A3	solute carrier family 27 member 3; fatty acid transport protein 3. [source:refseq;acc:nm_024330]	191.406	193.385	1.01034	
1904	SLC27A2	very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [source:swissprot;acc:o14975]	191.424	193.404	1.01034	
1905	UTP3	disrupter of silencing 10. [source:refseq;acc:nm_020368]	191.411	193.39	1.01034	
1906	SLC27A6	very long-chain acyl-coa synthetase homolog 1. [source:refseq;acc:nm_014031]	191.41	193.389	1.01034	
1907	SLC27A5	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [source:refseq;acc:nm_012254]	191.408	193.387	1.01034	

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/