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.


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 description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 2675 to 2724 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
2675	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [source:swissprot;acc:q9byn8]	215.108	214.893	1.001	
2676	enhancer of rudimentary homolog. [source:swissprot;acc:q14259]	215.108	214.893	1.001	
2677	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [source:swissprot;acc:q9uq13]	144.553	144.412	1.00098	
2678	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [source:swissprot;acc:o15211]	144.552	144.411	1.00098	
2679	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	189.959	190.142	1.00096	
2680	transforming protein p21/h-ras-1 (c-h-ras). [source:swissprot;acc:p01112]	144.56	144.422	1.00096	
2681	ubiquitin-specific protease otubain 2. [source:refseq;acc:nm_023112]	203.787	203.592	1.00096	
2682	transforming protein n-ras. [source:swissprot;acc:p01111]	144.564	144.427	1.00095	
2683	nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [source:swissprot;acc:p16991]	208.635	208.438	1.00095	
2684	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [source:swissprot;acc:p16989]	208.635	208.438	1.00095	
2685	germ cell specific y-box binding protein; contrin. [source:refseq;acc:nm_015982]	208.635	208.438	1.00095	
2686	proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [source:swissprot;acc:q99436]	219.629	219.829	1.00091	
2687	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [source:swissprot;acc:o15382]	210.755	210.939	1.00087	
2688	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [source:swissprot;acc:o75521]	194.392	194.557	1.00085	
2689	atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [source:swissprot;acc:p53396]	213.619	213.792	1.00081	
2690	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [source:swissprot;acc:p55087]	188.046	188.191	1.00077	
2691	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	188.048	188.193	1.00077	
2692	aquaporin 5. [source:swissprot;acc:p55064]	188.048	188.192	1.00077	
2693	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	188.049	188.193	1.00077	
2694	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [source:swissprot;acc:p29972]	188.081	188.223	1.00075	
2695	signal recognition particle 54 kda protein (srp54). [source:swissprot;acc:p13624]	215.384	215.545	1.00075	
2696	iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [source:swissprot;acc:p21399]	201.794	201.652	1.0007	
2697	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [source:swissprot;acc:o15144]	225.232	225.081	1.00067	
2698	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [source:swissprot;acc:p51571]	188.31	188.435	1.00066	
2699	calsyntenin-1 precursor. [source:swissprot;acc:o94985]	188.31	188.435	1.00066	
2700	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	188.31	188.435	1.00066	
2701	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [source:swissprot;acc:o15075]	216.682	216.539	1.00066	
2702	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	188.311	188.435	1.00066	
2703	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	188.311	188.435	1.00066	
2704	gk001 protein. [source:refseq;acc:nm_020198]	188.311	188.435	1.00066	
2705	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	188.334	188.457	1.00065	
2706	calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	188.336	188.459	1.00065	
2707	red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [source:swissprot;acc:p24666]	215.232	215.096	1.00063	
2708	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [source:swissprot;acc:p08397]	227.66	227.796	1.0006	
2709	importin 7; ran-binding protein 7. [source:refseq;acc:nm_006391]	220.395	220.521	1.00057	
2710	importin 8; ran-binding protein 8. [source:refseq;acc:nm_006390]	220.395	220.521	1.00057	
2711	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [source:swissprot;acc:q9y6d5]	220.395	220.521	1.00057	
2712	hsgcn1 (fragment). [source:sptrembl;acc:q99736]	220.395	220.521	1.00057	
2713	brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [source:swissprot;acc:q9y6d6]	220.395	220.521	1.00057	
2714	similar to trna synthetase class ii. [source:refseq;acc:nm_152268]	220.348	220.224	1.00056	
2715	basic proline-rich peptide p-e (ib-9). [source:swissprot;acc:p02811]	215.903	216.018	1.00053	
2716	salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [source:swissprot;acc:p10162]	215.903	216.018	1.00053	
2717	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [source:refseq;acc:nm_014268]	216.634	216.521	1.00052	
2718	histidine-rich membrane protein ke4. [source:swissprot;acc:q92504]	216.632	216.52	1.00052	
2719	microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [source:swissprot;acc:q15691]	216.632	216.52	1.00052	
2720	microtubule-associated protein rp/eb family member 3 (protein eb3). [source:swissprot;acc:q9upy8]	216.633	216.52	1.00052	
2721	bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [source:swissprot;acc:p07814]	221.116	221.022	1.00043	
2722	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [source:swissprot;acc:q9y4p3]	219.214	219.308	1.00043	
2723	lamin b2. [source:swissprot;acc:q03252]	219.413	219.323	1.00041	
2724	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [source:swissprot;acc:p08238]	220.963	221.053	1.00041	

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/