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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 1958 to 2007 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
1958	AKR7A3	aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [source:swissprot;acc:o95154]	211.633	213.703	1.00978	
1959	ABHD3	alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [source:refseq;acc:nm_138340]	211.633	213.703	1.00978	
1960	YIPF5	golgi membrane protein sb140; smooth muscle cell associated protein 5. [source:refseq;acc:nm_030799]	211.633	213.703	1.00978	
1961	ABHD1	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	ALDH6A1	methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [source:swissprot;acc:q02252]	211.632	213.702	1.00978	
1963	HSPE1	10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [source:swissprot;acc:q04984]	211.633	213.703	1.00978	
1964	RABAC1	rab acceptor 1 (prenylated); prenylated rab acceptor 1. [source:refseq;acc:nm_006423]	211.633	213.703	1.00978	
1965	ADD1	alpha adducin (erythrocyte adducin alpha subunit). [source:swissprot;acc:p35611]	224.432	222.258	1.00978	
1966	REXO2	oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [source:swissprot;acc:q9y3b8]	211.633	213.703	1.00978	
1967	CHAT	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [source:swissprot;acc:p28329]	211.632	213.702	1.00978	
1968	KCNAB2	voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [source:swissprot;acc:q13303]	211.633	213.703	1.00978	
1969	AKR7A2	aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [source:swissprot;acc:o43488]	211.633	213.703	1.00978	
1970	KPNA6	importin alpha-6 subunit (karyopherin alpha-5 subunit). [source:swissprot;acc:o15131]	211.62	213.683	1.00975	
1971	CKM	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [source:swissprot;acc:p06732]	198.258	196.346	1.00974	
1972	SEC16B	regucalcin gene promotor region related protein; rgpr-p117. [source: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). [source:swissprot;acc:q9y6w5]	214.611	212.546	1.00972	
1974	WASF3	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [source:swissprot;acc:q9upy6]	214.611	212.546	1.00972	
1975	WASF1	wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [source:swissprot;acc:q92558]	214.611	212.546	1.00972	
1976	RCOR1	rest corepressor. [source:refseq;acc:nm_015156]	214.611	212.546	1.00972	
1977	MAF1	homolog of yeast maf1. [source:refseq;acc:nm_032272]	209.539	207.529	1.00969	
1978	SERINC2	tumor differentially expressed protein 2. [source:refseq;acc:nm_178865]	209.539	207.529	1.00969	
1979	SERINC3	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [source:swissprot;acc:q13530]	209.539	207.529	1.00969	
1980	SERINC1	tumor differentially expressed 1 protein like. [source:swissprot;acc:q9nrx5]	209.539	207.529	1.00969	
1981	PHGDH	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [source:swissprot;acc:o43175]	209.539	207.529	1.00969	
1982		40s ribosomal protein s28. [source:swissprot;acc:p25112]	200.343	198.427	1.00966	
1983	PDLIM5	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [source:refseq;acc:nm_006457]	219.25	217.175	1.00955	
1984	EP400	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [source:refseq;acc:nm_015409]	219.26	217.193	1.00952	
1985	MRPL24	mitochondrial ribosomal protein l24. [source:refseq;acc:nm_024540]	219.26	217.193	1.00952	
1986	YAP1	65 kda yes-associated protein (yap65). [source:swissprot;acc:p46937]	219.26	217.193	1.00952	
1987	LIN7A	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [source:refseq;acc:nm_004664]	225.022	222.9	1.00952	
1988	CCDC130	9 kda protein. [source:swissprot;acc:p13994]	219.26	217.193	1.00952	
1989	COL4A3	collagen alpha 3(iv) chain precursor (goodpasture antigen). [source:swissprot;acc:q01955]	219.261	217.195	1.00951	
1990		collagen alpha 5(iv) chain precursor. [source:swissprot;acc:p29400]	219.26	217.194	1.00951	
1991	WWTR1	transcriptional co-activator with pdz-binding motif (taz). [source:refseq;acc:nm_015472]	219.26	217.194	1.00951	
1992	LDB3	zasp protein (fragment). [source:sptrembl;acc:q9y4z3]	219.267	217.207	1.00948	
1993	HIP1R	huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	189.052	190.835	1.00943	
1994	COL4A3BP	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). [source:swissprot;acc:q9y5p4]	189.011	190.787	1.0094	
1995	HIP1	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	188.961	190.73	1.00936	
1996	SLC5A5	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [source:swissprot;acc:q92911]	204.682	202.784	1.00936	
1997	PRODH2	kidney and liver proline oxidase 1. [source:refseq;acc:nm_021232]	204.651	202.759	1.00933	
1998	C15orf15	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	200.219	198.37	1.00932	
1999	SLC5A8	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [source:refseq;acc:nm_145913]	204.636	202.748	1.00931	
2000	SLC5A6	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [source:swissprot;acc:q9y289]	204.626	202.739	1.00931	
2001	LIN7B	lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [source:refseq;acc:nm_022165]	225.02	222.948	1.00929	
2002	SNRPB2	u2 small nuclear ribonucleoprotein b". [source:swissprot;acc:p08579]	214.775	216.769	1.00928	
2003	DNALI1	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [source:swissprot;acc:o14645]	208.315	206.41	1.00923	
2004	ERBB4	receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [source:swissprot;acc:q15303]	225.019	222.969	1.00919	
2005	EGFR	epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [source:swissprot;acc:p00533]	225.019	222.971	1.00919	
2006	ERBB2	receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [source:swissprot;acc:p04626]	225.019	222.971	1.00919	
2007	HACL1	2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [source:swissprot;acc:q9uj83]	225.019	222.969	1.00919	

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/