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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2001 to 2050 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
1001	DCT	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [source:swissprot;acc:p40126]	Subtracted	221.28	214.409	6.871	
1001	SPRY3	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	Divided	225.167	217.922	1.03325	
1002	SPRY1	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	Divided	225.167	217.922	1.03325	
1002	TYRP1	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	Subtracted	221.278	214.409	6.869	
1003	PNN	pinin, desmosome associated protein; pinin. [source:refseq;acc:nm_002687]	Subtracted	211.071	204.205	6.866	
1003	SPRY2	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	Divided	225.167	217.922	1.03325	
1004		sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	Divided	238.725	231.059	1.03318	
1004	FHL3	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [source:swissprot;acc:q13643]	Subtracted	269.59	276.454	6.864	
1005	DKC1	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	Subtracted	231.007	237.864	6.857	
1005	DYNC1I1	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	Divided	225.448	218.232	1.03307	
1006	CPSF3	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	Divided	116.524	120.375	1.03305	
1006	RBL2	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	Subtracted	217.026	210.189	6.837	
1007	RALGDS	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Divided	162.055	156.884	1.03296	
1007	RBL1	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	Subtracted	217.021	210.185	6.836	
1008	DDB1	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [source:swissprot;acc:q16531]	Subtracted	222.364	215.535	6.829	
1008	WDR46	wd-repeat protein bing4. [source:swissprot;acc:o15213]	Divided	243.227	235.475	1.03292	
1009		dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Divided	229.116	221.823	1.03288	
1009	PCCB	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [source:swissprot;acc:p05166]	Subtracted	222.364	215.535	6.829	
1010	ATXN2L	ataxin 2 related protein isoform a; ataxin-2 domain protein. [source:refseq;acc:nm_007245]	Subtracted	228.105	221.293	6.812	
1010	CROT	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [source:swissprot;acc:q9ukg9]	Divided	217.523	210.648	1.03264	
1011		ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	Subtracted	228.105	221.293	6.812	
1011	RBL2	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	Divided	217.026	210.189	1.03253	
1012	KPNA4	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	Subtracted	217.369	210.561	6.808	
1012	RBL1	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	Divided	217.021	210.185	1.03252	
1013	HEATR1	protein bap28. [source:swissprot;acc:q9h583]	Divided	244.312	236.647	1.03239	
1013	TOE1	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	Subtracted	217.365	210.558	6.807	
1014	AATF	apoptosis antagonizing transcription factor. [source:refseq;acc:nm_012138]	Divided	243.045	235.422	1.03238	
1014	KPNA3	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	Subtracted	217.361	210.554	6.807	
1015	EXOC3	exocyst complex component sec6. [source:swissprot;acc:o60645]	Subtracted	207.186	200.398	6.788	
1015	MAGI1	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [source:refseq;acc:nm_004742]	Divided	221.73	228.906	1.03236	
1016	KPNA4	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	Divided	217.369	210.561	1.03233	
1016	TYR	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [source:swissprot;acc:p14679]	Subtracted	221.183	214.406	6.777	
1017	SUCLG1	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [source:swissprot;acc:p53597]	Subtracted	211.908	218.627	6.719	
1017	TOE1	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	Divided	217.365	210.558	1.03233	
1018	KPNA3	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	Divided	217.361	210.554	1.03233	
1018	SUCLA2	succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [source:swissprot;acc:q9p2r7]	Subtracted	211.908	218.627	6.719	
1019		60s ribosomal protein l21. [source:swissprot;acc:p46778]	Subtracted	223.958	217.263	6.695	
1019	TYRL	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	Divided	221.302	214.409	1.03215	
1020		similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	Subtracted	226.218	232.88	6.662	
1020	DCT	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [source:swissprot;acc:p40126]	Divided	221.28	214.409	1.03205	
1021		block 23. [source:sptrembl;acc:q8nhw5]	Subtracted	226.205	232.858	6.653	
1021	TYRP1	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	Divided	221.278	214.409	1.03204	
1022	CBS	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	Divided	205.632	199.266	1.03195	
1022	RPLP0	60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	Subtracted	226.203	232.855	6.652	
1023	BLOC1S1	gcn5-like protein 1 (rt14 protein). [source:swissprot;acc:p78537]	Subtracted	202.027	195.386	6.641	
1023	RHOC	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	Divided	205.632	199.266	1.03195	
1024	DPM1	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	Subtracted	203.381	196.76	6.621	
1024	TST	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	Divided	205.632	199.266	1.03195	
1025	FAU	40s ribosomal protein s30. [source:swissprot;acc:q05472]	Subtracted	223.44	216.875	6.565	
1025	MPST	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	Divided	205.632	199.266	1.03195	

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/