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	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 1951 to 2000 of 3228 in total

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

Rank	description	green	red	network_comparison
1951	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	203.873	205.876	1.00982
1952	importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294]	213.724	211.647	1.00981
1953	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	127.146	125.912	1.0098
1954	voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448]	213.703	211.632	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]	213.702	211.632
1963	10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	213.703	211.633
1964	rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423]
1965	alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611]	222.258	224.432
1966	oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8]	213.703	211.633
1967	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]	213.702	211.632
1968	voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303]	213.703	211.633
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]	213.683	211.62	1.00975
1971	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732]	196.346	198.258	1.00974
1972	regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127]	217.659	219.777	1.00973
1973	wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5]	212.546	214.611	1.00972
1974	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]
1975	wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558]
1976	rest corepressor. [refseq;acc:nm_015156]
1977	homolog of yeast maf1. [refseq;acc:nm_032272]	207.529	209.539	1.00969
1978	tumor differentially expressed protein 2. [refseq;acc:nm_178865]
1979	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530]
1980	tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]
1981	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
1982	40s ribosomal protein s28. [swissprot;acc:p25112]	198.427	200.343	1.00966
1983	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	217.175	219.25	1.00955
1984	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	217.193	219.26	1.00952
1985	mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]
1986	65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
1987	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664]	222.9	225.022
1988	9 kda protein. [swissprot;acc:p13994]	217.193	219.26
1989	collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955]	217.195	219.261	1.00951
1990	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	217.194	219.26
1991	transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]
1992	zasp protein (fragment). [sptrembl;acc:q9y4z3]	217.207	219.267	1.00948
1993	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	190.835	189.052	1.00943
1994	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	190.787	189.011	1.0094
1995	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	190.73	188.961	1.00936
1996	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	202.784	204.682
1997	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	202.759	204.651	1.00933
1998	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	198.37	200.219	1.00932
1999	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	202.748	204.636	1.00931
2000	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	202.739	204.626

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.