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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2677 to 2726 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
2677	SHOC2	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [source:swissprot;acc:q9uq13]	144.412	144.553	1.00098	
2678		ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [source:swissprot;acc:o15211]	144.411	144.552	1.00098	
2679	ANAPC2	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	190.142	189.959	1.00096	
2680	HRAS	transforming protein p21/h-ras-1 (c-h-ras). [source:swissprot;acc:p01112]	144.422	144.56	1.00096	
2681	OTUB2	ubiquitin-specific protease otubain 2. [source:refseq;acc:nm_023112]	203.592	203.787	1.00096	
2682		transforming protein n-ras. [source:swissprot;acc:p01111]	144.427	144.564	1.00095	
2683	YBX1	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]	208.438	208.635	1.00095	
2684	CSDA	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [source:swissprot;acc:p16989]	208.438	208.635	1.00095	
2685	YBX2	germ cell specific y-box binding protein; contrin. [source:refseq;acc:nm_015982]	208.438	208.635	1.00095	
2686	PSMB7	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]	219.829	219.629	1.00091	
2687	BCAT2	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [source:swissprot;acc:o15382]	210.939	210.755	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]	194.557	194.392	1.00085	
2689	ACLY	atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [source:swissprot;acc:p53396]	213.792	213.619	1.00081	
2690	AQP4	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [source:swissprot;acc:p55087]	188.191	188.046	1.00077	
2691	AQP2	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]	188.193	188.048	1.00077	
2692	AQP5	aquaporin 5. [source:swissprot;acc:p55064]	188.192	188.048	1.00077	
2693	MIP	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	188.193	188.049	1.00077	
2694	AQP1	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [source:swissprot;acc:p29972]	188.223	188.081	1.00075	
2695	SRP54	signal recognition particle 54 kda protein (srp54). [source:swissprot;acc:p13624]	215.545	215.384	1.00075	
2696	ACO1	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]	201.652	201.794	1.0007	
2697	ARPC2	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [source:swissprot;acc:o15144]	225.081	225.232	1.00067	
2698	SSR4	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [source:swissprot;acc:p51571]	188.435	188.31	1.00066	
2699	CLSTN1	calsyntenin-1 precursor. [source:swissprot;acc:o94985]	188.435	188.31	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]	188.435	188.31	1.00066	
2701	DCLK1	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [source:swissprot;acc:o15075]	216.539	216.682	1.00066	
2702	PTPRB	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	188.435	188.311	1.00066	
2703	PRSS16	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	188.435	188.311	1.00066	
2704	CCDC47	gk001 protein. [source:refseq;acc:nm_020198]	188.435	188.311	1.00066	
2705	CLSTN2	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	188.457	188.334	1.00065	
2706	CLSTN3	calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	188.459	188.336	1.00065	
2707	ACP1	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]	215.096	215.232	1.00063	
2708	HMBS	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [source:swissprot;acc:p08397]	227.796	227.66	1.0006	
2709		importin 7; ran-binding protein 7. [source:refseq;acc:nm_006391]	220.521	220.395	1.00057	
2710	IPO8	importin 8; ran-binding protein 8. [source:refseq;acc:nm_006390]	220.521	220.395	1.00057	
2711	ARFGEF2	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [source:swissprot;acc:q9y6d5]	220.521	220.395	1.00057	
2712	GCN1L1	hsgcn1 (fragment). [source:sptrembl;acc:q99736]	220.521	220.395	1.00057	
2713	ARFGEF1	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]	220.521	220.395	1.00057	
2714	PARS2	similar to trna synthetase class ii. [source:refseq;acc:nm_152268]	220.224	220.348	1.00056	
2715		basic proline-rich peptide p-e (ib-9). [source:swissprot;acc:p02811]	216.018	215.903	1.00053	
2716	PRB4	salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [source:swissprot;acc:p10162]	216.018	215.903	1.00053	
2717	MAPRE2	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [source:refseq;acc:nm_014268]	216.521	216.634	1.00052	
2718	SLC39A7	histidine-rich membrane protein ke4. [source:swissprot;acc:q92504]	216.52	216.632	1.00052	
2719	MAPRE1	microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [source:swissprot;acc:q15691]	216.52	216.632	1.00052	
2720	MAPRE3	microtubule-associated protein rp/eb family member 3 (protein eb3). [source:swissprot;acc:q9upy8]	216.52	216.633	1.00052	
2721	EPRS	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]	221.022	221.116	1.00043	
2722	TBL2	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [source:swissprot;acc:q9y4p3]	219.308	219.214	1.00043	
2723		lamin b2. [source:swissprot;acc:q03252]	219.323	219.413	1.00041	
2724	HSP90AB1	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [source:swissprot;acc:p08238]	221.053	220.963	1.00041	
2725	DCX	doublecortin (lissencephalin-x) (lis-x) (doublin). [source:swissprot;acc:o43602]	216.496	216.569	1.00034	
2726	RAD17	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [source:refseq;acc:nm_002873]	221.001	220.927	1.00033	

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/