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.


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 Network Comparison Type Value Type description Filtered Interaction Map network_comparison green red
Results: HTML CSV LaTeX Showing element 1963 to 2012 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Filtered	1
Interaction Map	High confidence

Rank	description	network_comparison	green	red	
1963	10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [source:swissprot;acc:q04984]	1.00978	213.703	211.633	
1964	rab acceptor 1 (prenylated); prenylated rab acceptor 1. [source:refseq;acc:nm_006423]	1.00978	213.703	211.633	
1965	alpha adducin (erythrocyte adducin alpha subunit). [source:swissprot;acc:p35611]	1.00978	222.258	224.432	
1966	oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [source:swissprot;acc:q9y3b8]	1.00978	213.703	211.633	
1967	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [source:swissprot;acc:p28329]	1.00978	213.702	211.632	
1968	voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [source:swissprot;acc:q13303]	1.00978	213.703	211.633	
1969	aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [source:swissprot;acc:o43488]	1.00978	213.703	211.633	
1970	importin alpha-6 subunit (karyopherin alpha-5 subunit). [source:swissprot;acc:o15131]	1.00975	213.683	211.62	
1971	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [source:swissprot;acc:p06732]	1.00974	196.346	198.258	
1972	regucalcin gene promotor region related protein; rgpr-p117. [source:refseq;acc:nm_033127]	1.00973	217.659	219.777	
1973	wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [source:swissprot;acc:q9y6w5]	1.00972	212.546	214.611	
1974	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [source:swissprot;acc:q9upy6]	1.00972	212.546	214.611	
1975	wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [source:swissprot;acc:q92558]	1.00972	212.546	214.611	
1976	rest corepressor. [source:refseq;acc:nm_015156]	1.00972	212.546	214.611	
1977	homolog of yeast maf1. [source:refseq;acc:nm_032272]	1.00969	207.529	209.539	
1978	tumor differentially expressed protein 2. [source:refseq;acc:nm_178865]	1.00969	207.529	209.539	
1979	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [source:swissprot;acc:q13530]	1.00969	207.529	209.539	
1980	tumor differentially expressed 1 protein like. [source:swissprot;acc:q9nrx5]	1.00969	207.529	209.539	
1981	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [source:swissprot;acc:o43175]	1.00969	207.529	209.539	
1982	40s ribosomal protein s28. [source:swissprot;acc:p25112]	1.00966	198.427	200.343	
1983	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [source:refseq;acc:nm_006457]	1.00955	217.175	219.25	
1984	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [source:refseq;acc:nm_015409]	1.00952	217.193	219.26	
1985	mitochondrial ribosomal protein l24. [source:refseq;acc:nm_024540]	1.00952	217.193	219.26	
1986	65 kda yes-associated protein (yap65). [source:swissprot;acc:p46937]	1.00952	217.193	219.26	
1987	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [source:refseq;acc:nm_004664]	1.00952	222.9	225.022	
1988	9 kda protein. [source:swissprot;acc:p13994]	1.00952	217.193	219.26	
1989	collagen alpha 3(iv) chain precursor (goodpasture antigen). [source:swissprot;acc:q01955]	1.00951	217.195	219.261	
1990	collagen alpha 5(iv) chain precursor. [source:swissprot;acc:p29400]	1.00951	217.194	219.26	
1991	transcriptional co-activator with pdz-binding motif (taz). [source:refseq;acc:nm_015472]	1.00951	217.194	219.26	
1992	zasp protein (fragment). [source:sptrembl;acc:q9y4z3]	1.00948	217.207	219.267	
1993	huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	1.00943	190.835	189.052	
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). [source:swissprot;acc:q9y5p4]	1.0094	190.787	189.011	
1995	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	1.00936	190.73	188.961	
1996	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [source:swissprot;acc:q92911]	1.00936	202.784	204.682	
1997	kidney and liver proline oxidase 1. [source:refseq;acc:nm_021232]	1.00933	202.759	204.651	
1998	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	1.00932	198.37	200.219	
1999	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [source:refseq;acc:nm_145913]	1.00931	202.748	204.636	
2000	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [source:swissprot;acc:q9y289]	1.00931	202.739	204.626	
2001	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]	1.00929	222.948	225.02	
2002	u2 small nuclear ribonucleoprotein b". [source:swissprot;acc:p08579]	1.00928	216.769	214.775	
2003	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [source:swissprot;acc:o14645]	1.00923	206.41	208.315	
2004	receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [source:swissprot;acc:q15303]	1.00919	222.969	225.019	
2005	epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [source:swissprot;acc:p00533]	1.00919	222.971	225.019	
2006	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]	1.00919	222.971	225.019	
2007	2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [source:swissprot;acc:q9uj83]	1.00919	222.969	225.019	
2008	receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [source:swissprot;acc:p21860]	1.00919	222.969	225.019	
2009	proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [source:swissprot;acc:p40306]	1.00913	214.245	216.201	
2010	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [source:swissprot;acc:q15814]	1.00913	191.766	193.517	
2011	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [source:swissprot;acc:q9y305]	1.00913	191.766	193.517	
2012	dead-box protein. [source:refseq;acc:nm_018665]	1.00913	191.766	193.517	

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/