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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1913 to 1962 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1913	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [source:swissprot;acc:q9nry6]	215.745	213.564	1.01021	
1914	phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [source:swissprot;acc:q9nrq2]	215.745	213.564	1.01021	
1915	phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [source:swissprot;acc:q9nry7]	215.747	213.571	1.01019	
1916	rh type c glycoprotein. [source:refseq;acc:nm_016321]	196.88	198.88	1.01016	
1917	p28 ing5. [source:refseq;acc:nm_032329]	215.848	218.039	1.01015	
1918	endothelial-derived gene 1. [source:refseq;acc:nm_025205]	202.211	200.18	1.01015	
1919	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	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	187.292	185.413	1.01013	
1921	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	centaurin gamma 2. [source:swissprot;acc:q9upq3]	220.659	218.452	1.0101	
1923	general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [source:swissprot;acc:o60763]	220.659	218.452	1.0101	
1924	centaurin gamma 1. [source:swissprot;acc:q99490]	220.659	218.452	1.0101	
1925	centaurin gamma 3. [source:swissprot;acc:q96p47]	220.659	218.452	1.0101	
1926	rhesus blood group, b glycoprotein; rh type b glycoprotein. [source:refseq;acc:nm_020407]	196.925	198.91	1.01008	
1927	rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [source:swissprot;acc:q02094]	196.932	198.914	1.01006	
1928	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	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	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [source:swissprot;acc:p00480]	215.667	217.82	1.00998	
1934	gamma adducin (adducin-like protein 70). [source:swissprot;acc:q9uey8]	224.264	222.055	1.00995	
1935	abhydrolase domain containing protein 2 (protein phps1-2). [source:swissprot;acc:p08910]	218.43	216.279	1.00995	
1936	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	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	peptidyl prolyl isomerase h; cyclophilin h. [source:refseq;acc:nm_006347]	198.258	196.319	1.00988	
1940	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [source:swissprot;acc:p12277]	198.19	196.252	1.00988	
1941	prp18 pre-mrna processing factor 18 homolog. [source:refseq;acc:nm_003675]	198.258	196.319	1.00988	
1942	j domain protein c21orf55. [source:swissprot;acc:q9nx36]	198.257	196.319	1.00987	
1943	megf11 protein. [source:refseq;acc:nm_032445]	224.34	222.147	1.00987	
1944	megf10 protein. [source:refseq;acc:nm_032446]	224.341	222.148	1.00987	
1945	beta adducin (erythrocyte adducin beta subunit). [source:swissprot;acc:p35612]	224.343	222.151	1.00987	
1946	nuclear factor, interleukin 3 regulated. [source:refseq;acc:nm_005384]	214.234	212.142	1.00986	
1947	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	rna-binding protein with multiple splicing (rbp-ms). [source:swissprot;acc:q93062]	218.794	216.663	1.00984	
1950	vacuolar protein sorting 18 (hvps18). [source:swissprot;acc:q9p253]	215.847	213.747	1.00982	
1951	trna isopentenylpyrophosphate transferase. [source:refseq;acc:nm_017646]	205.876	203.873	1.00982	
1952	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	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	125.912	127.146	1.0098	
1954	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	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	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	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	
1958	aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [source:swissprot;acc:o95154]	211.633	213.703	1.00978	
1959	alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [source:refseq;acc:nm_138340]	211.633	213.703	1.00978	
1960	golgi membrane protein sb140; smooth muscle cell associated protein 5. [source:refseq;acc:nm_030799]	211.633	213.703	1.00978	
1961	alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [source:refseq;acc:nm_152870]	211.633	213.703	1.00978	
1962	methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [source:swissprot;acc:q02252]	211.632	213.702	1.00978	

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/