MK5 Microarray Data

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 1925 to 1974 of 3228 in total

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

Rank	description	red	green	network_comparison
1925	centaurin gamma 3. [swissprot;acc:q96p47]	220.659	218.452	1.0101
1926	rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407]	196.925	198.91	1.01008
1927	rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094]	196.932	198.914	1.01006
1928	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	196.964	198.935	1.01001
1929	enigma protein; lim domain protein. [refseq;acc:nm_005451]	219.753	217.574
1930	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	196.964	198.935
1931	eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371]	219.753	217.574
1932	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	196.965	198.936
1933	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480]	215.667	217.82	1.00998
1934	gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8]	224.264	222.055	1.00995
1935	abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910]	218.43	216.279
1936	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540]	198.3	196.347
1937	quaking isoform 6. [sptrembl;acc:q9p0x9]	218.43	216.279
1938	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	198.293	196.341	1.00994
1939	peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347]	198.258	196.319	1.00988
1940	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]	198.19	196.252
1941	prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675]	198.258	196.319
1942	j domain protein c21orf55. [swissprot;acc:q9nx36]	198.257		1.00987
1943	megf11 protein. [refseq;acc:nm_032445]	224.34	222.147
1944	megf10 protein. [refseq;acc:nm_032446]	224.341	222.148
1945	beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612]	224.343	222.151
1946	nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384]	214.234	212.142	1.00986
1947	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	125.845	127.083	1.00984
1948	15 kda selenoprotein precursor. [swissprot;acc:o60613]	214.522	212.432
1949	rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062]	218.794	216.663
1950	vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253]	215.847	213.747	1.00982
1951	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	205.876	203.873
1952	importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294]	211.647	213.724	1.00981
1953	type 1 protein phosphatase inhibitor. [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). [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. [refseq;acc:nm_020470]	211.633		1.00978
1956	voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722]
1957	similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557]
1958	aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]
1959	alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340]
1960	golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799]
1961	alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870]
1962	methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252]	211.632	213.702
1963	10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	211.633	213.703
1964	rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423]
1965	alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611]	224.432	222.258
1966	oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8]	211.633	213.703
1967	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]	211.632	213.702
1968	voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303]	211.633	213.703
1969	aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
1970	importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131]	211.62	213.683	1.00975
1971	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732]	198.258	196.346	1.00974
1972	regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127]	219.777	217.659	1.00973
1973	wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5]	214.611	212.546	1.00972
1974	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.