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 2233 to 2282 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison	
2233	TRIM3	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [source:swissprot;acc:o75382]	202.414	203.691	1.00631	
2234		seven in absentia homolog 1. [source:refseq;acc:nm_003031]	223.608	225.005	1.00625	
2235	RARS2	arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	200.95	199.711	1.0062	
2236		protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [source:refseq;acc:nm_003981]	222.959	224.337	1.00618	
2237	BRD3	bromodomain-containing protein 3 (ring3-like protein). [source:swissprot;acc:q15059]	222.965	224.343	1.00618	
2238	BRD4	bromodomain-containing protein 4 (hunk1 protein). [source:swissprot;acc:o60885]	222.959	224.337	1.00618	
2239	BRDT	testis-specific bromodomain protein. [source:refseq;acc:nm_001726]	222.958	224.336	1.00618	
2240	LRRC4	nag14 protein. [source:refseq;acc:nm_022143]	222.959	224.337	1.00618	
2241	BRD2	bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [source:swissprot;acc:p25440]	222.96	224.338	1.00618	
2242	ITM2B	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [source:swissprot;acc:q9y287]	209.197	207.915	1.00617	
2243	ITM2C	integral membrane protein 2c (transmembrane protein bri3) (npd018). [source:swissprot;acc:q9nqx7]	209.197	207.915	1.00617	
2244	ITM2A	integral membrane protein 2a (e25 protein). [source:swissprot;acc:o43736]	209.197	207.915	1.00617	
2245	FBLN2	fibulin-2 precursor. [source:swissprot;acc:p98095]	191.618	190.448	1.00614	
2246	MRPL18	mitochondrial ribosomal protein l18. [source:refseq;acc:nm_014161]	223.58	224.943	1.0061	
2247	ADI1	sipl protein. [source:refseq;acc:nm_018269]	208.609	207.346	1.00609	
2248	KIF3C	kinesin-like protein kif3c. [source:swissprot;acc:o14782]	219.045	220.377	1.00608	
2249	PC	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498]	181.091	179.999	1.00607	
2250	CSTF2T	likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235]	164.064	165.058	1.00606	
2251	ENOPH1	e-1 enzyme. [source:refseq;acc:nm_021204]	208.315	207.061	1.00606	
2252	ALAD	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [source:swissprot;acc:p13716]	217.185	218.498	1.00605	
2253	KIF3B	kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [source:swissprot;acc:o15066]	219.047	220.371	1.00604	
2254		ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [source:swissprot;acc:p47986]	193.065	194.22	1.00598	
2255	ZFHX3	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [source:swissprot;acc:q15911]	202.366	203.57	1.00595	
2256	SIAH2	seven in absentia homolog 2. [source:refseq;acc:nm_005067]	223.546	224.869	1.00592	
2257	QPRT	nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [source:swissprot;acc:q15274]	212.563	211.315	1.00591	
2258	CDC37	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [source:swissprot;acc:q16543]	223.888	225.191	1.00582	
2259	DMC1	meiotic recombination protein dmc1/lim15 homolog. [source:swissprot;acc:q14565]	213.391	214.606	1.00569	
2260	TSEN34	leng5 protein. [source:refseq;acc:nm_024075]	221.599	220.351	1.00566	
2261	WARS	tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [source:swissprot;acc:p23381]	221.599	220.351	1.00566	
2262		ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [source:refseq;acc:nm_006916]	221.599	220.351	1.00566	
2263	WARS2	tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [source:swissprot;acc:q9ugm6]	221.599	220.351	1.00566	
2264		thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [source:refseq;acc:nm_022445]	221.599	220.351	1.00566	
2265	MAD2L1	mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [source:swissprot;acc:q13257]	211.597	210.416	1.00561	
2266	ATP13A2	probable cation-transporting atpase 1 (ec 3.6.1.-). [source:swissprot;acc:q9nq11]	211.597	210.416	1.00561	
2267	TBP	tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [source:swissprot;acc:p20226]	211.597	210.416	1.00561	
2268	TRIM2	tripartite motif protein 2. [source:swissprot;acc:q9c040]	202.312	203.437	1.00556	
2269	PSMD10	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	217.419	218.627	1.00556	
2270	MMS19	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [source:refseq;acc:nm_022362]	207.54	208.69	1.00554	
2271	FMO5	dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [source:swissprot;acc:p49326]	216.622	215.436	1.00551	
2272	FMO6P	putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [source:swissprot;acc:o60774]	216.622	215.436	1.00551	
2273	MAP3K7IP1	mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [source:swissprot;acc:q15750]	213.015	211.858	1.00546	
2274	PGD	6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	213.642	214.801	1.00542	
2275	DHDDS	dehydrodolichyl diphosphate synthase. [source:refseq;acc:nm_024887]	207.319	208.44	1.00541	
2276	FMO3	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	216.613	215.448	1.00541	
2277	RCC1	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	191.936	190.909	1.00538	
2278	ZEB2	zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [source:swissprot;acc:o60315]	191.936	190.909	1.00538	
2279	ZEB1	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [source:swissprot;acc:p37275]	191.936	190.909	1.00538	
2280	PSMA7	proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [source:swissprot;acc:o14818]	212.793	211.657	1.00537	
2281	SRRM2	splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [source:refseq;acc:nm_016333]	219.652	218.482	1.00536	
2282	U2AF1	splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [source:swissprot;acc:q01081]	219.652	218.482	1.00536	

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/