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 1908 to 1957 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison	
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	
1925	CENTG3	centaurin gamma 3. [source:swissprot;acc:q96p47]	220.659	218.452	1.0101	
1926	RHBG	rhesus blood group, b glycoprotein; rh type b glycoprotein. [source:refseq;acc:nm_020407]	196.925	198.91	1.01008	
1927	RHAG	rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [source:swissprot;acc:q02094]	196.932	198.914	1.01006	
1928	RHD	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [source:swissprot;acc:q02161]	196.964	198.935	1.01001	
1929		enigma protein; lim domain protein. [source:refseq;acc:nm_005451]	219.753	217.574	1.01001	
1930		blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [source:swissprot;acc:p18577]	196.964	198.935	1.01001	
1931	EIF3D	eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [source:swissprot;acc:o15371]	219.753	217.574	1.01001	
1932		blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [source:swissprot;acc:p18577]	196.965	198.936	1.01001	
1933	OTC	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [source:swissprot;acc:p00480]	215.667	217.82	1.00998	
1934	ADD3	gamma adducin (adducin-like protein 70). [source:swissprot;acc:q9uey8]	224.264	222.055	1.00995	
1935	ABHD2	abhydrolase domain containing protein 2 (protein phps1-2). [source:swissprot;acc:p08910]	218.43	216.279	1.00995	
1936	CKMT2	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [source:swissprot;acc:p17540]	198.3	196.347	1.00995	
1937	QKI	quaking isoform 6. [source:sptrembl;acc:q9p0x9]	218.43	216.279	1.00995	
1938		creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	198.293	196.341	1.00994	
1939	PPIH	peptidyl prolyl isomerase h; cyclophilin h. [source:refseq;acc:nm_006347]	198.258	196.319	1.00988	
1940	CKB	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [source:swissprot;acc:p12277]	198.19	196.252	1.00988	
1941	PRPF18	prp18 pre-mrna processing factor 18 homolog. [source:refseq;acc:nm_003675]	198.258	196.319	1.00988	
1942	C21orf55	j domain protein c21orf55. [source:swissprot;acc:q9nx36]	198.257	196.319	1.00987	
1943	MEGF11	megf11 protein. [source:refseq;acc:nm_032445]	224.34	222.147	1.00987	
1944	MEGF10	megf10 protein. [source:refseq;acc:nm_032446]	224.341	222.148	1.00987	
1945	ADD2	beta adducin (erythrocyte adducin beta subunit). [source:swissprot;acc:p35612]	224.343	222.151	1.00987	
1946	NFIL3	nuclear factor, interleukin 3 regulated. [source:refseq;acc:nm_005384]	214.234	212.142	1.00986	
1947	PPP1R2	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	125.845	127.083	1.00984	
1948		15 kda selenoprotein precursor. [source:swissprot;acc:o60613]	214.522	212.432	1.00984	
1949	RBPMS	rna-binding protein with multiple splicing (rbp-ms). [source:swissprot;acc:q93062]	218.794	216.663	1.00984	
1950	VPS18	vacuolar protein sorting 18 (hvps18). [source:swissprot;acc:q9p253]	215.847	213.747	1.00982	
1951	TRIT1	trna isopentenylpyrophosphate transferase. [source:refseq;acc:nm_017646]	205.876	203.873	1.00982	
1952	KPNA1	importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [source:swissprot;acc:p52294]	211.647	213.724	1.00981	
1953	PPP1R2P9	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	125.912	127.146	1.0098	
1954	KCNAB3	voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [source:swissprot;acc:o43448]	211.632	213.703	1.00979	
1955	YIF1A	yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [source:refseq;acc:nm_020470]	211.633	213.703	1.00978	
1956	KCNAB1	voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [source:swissprot;acc:q14722]	211.633	213.703	1.00978	
1957	YIF1B	similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [source:refseq;acc:nm_033557]	211.633	213.703	1.00978	

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/