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 1875 to 1924 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison	
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	
1908	DIP2B	similar to cg7020 gene product (fragment). [source:sptrembl;acc:q96ib4]	191.415	193.394	1.01034	
1909	CLGN	calmegin precursor. [source:swissprot;acc:o14967]	217.48	215.256	1.01033	
1910	CANX	calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [source:swissprot;acc:p27824]	217.48	215.256	1.01033	
1911	SEPSECS	soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	217.48	215.256	1.01033	
1912	RNMT	rna (guanine-7-) methyltransferase. [source:refseq;acc:nm_003799]	217.48	215.256	1.01033	
1913		phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [source:swissprot;acc:q9nry6]	215.745	213.564	1.01021	
1914	PLSCR4	phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [source:swissprot;acc:q9nrq2]	215.745	213.564	1.01021	
1915	PLSCR2	phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [source:swissprot;acc:q9nry7]	215.747	213.571	1.01019	
1916	RHCG	rh type c glycoprotein. [source:refseq;acc:nm_016321]	196.88	198.88	1.01016	
1917	ING5	p28 ing5. [source:refseq;acc:nm_032329]	215.848	218.039	1.01015	
1918	MED28	endothelial-derived gene 1. [source:refseq;acc:nm_025205]	202.211	200.18	1.01015	
1919	HARS2	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	187.231	185.349	1.01015	
1920	HARS	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	187.292	185.413	1.01013	
1921	MTR	5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [source:swissprot;acc:q99707]	221.607	219.386	1.01012	
1922	CENTG2	centaurin gamma 2. [source:swissprot;acc:q9upq3]	220.659	218.452	1.0101	
1923	USO1	general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [source:swissprot;acc:o60763]	220.659	218.452	1.0101	
1924	CENTG1	centaurin gamma 1. [source:swissprot;acc:q99490]	220.659	218.452	1.0101	

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/