MK5 Microarray Data

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

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Rank	Gene	description	Hugo	Network Comparison Type	Value Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1430 to 1479 of 8289 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1

Rank	description	Hugo	Interaction Map	red	green	network_comparison
715	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]	GARS	Low confidence	203.107	197.646	1.02763
716	cpz gene product. [refseq;acc:nm_003652]	CPZ	High confidence	223.121	211.685	1.05402
	elongation factor 1-delta (ef-1-delta) (antigen ny-co-4). [swissprot;acc:p29692]	EEF1D	Low confidence	203.552	198.081	1.02762
717	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	CPE	High confidence	223.121	211.685	1.05402
	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	BTF3	Low confidence	204.133	198.652	1.02759
718	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	ARPC1B		201.612	196.213	1.02752
	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	CPXM1	High confidence	223.121	211.685	1.05402
719	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	NOL5A		247.769	235.074	1.054
	stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861]	STUB1	Low confidence	199.172	193.841	1.0275
720	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	RPLP2	High confidence	231.92	244.435	1.05396
	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	POLE	Low confidence	204.279	198.814	1.02749
721	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	EXOC5	High confidence	214.765	203.8	1.0538
	sorting nexin 16. [swissprot;acc:p57768]	SNX16	Low confidence	203.411	197.971	1.02748
722	igf-ii mrna-binding protein 1. [refseq;acc:nm_006546]	IGF2BP1		205.571	200.075	1.02747
	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	TREH	High confidence	217.952	206.902	1.05341
723	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	no value		244.842	232.577	1.05274
	poly(a)-specific ribonuclease (deadenylation nuclease); deadenylation nuclease. [refseq;acc:nm_002582]	PARN	Low confidence	203.779	198.331	1.02747
724	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]	ACY1		201.765	196.371
	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	no value	High confidence	244.842	232.577	1.05274
725	igf-ii mrna-binding protein 3; kh domain containing protein overexpressed in cancer. [refseq;acc:nm_006547]	IGF2BP3	Low confidence	205.563	200.075	1.02743
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	MVK	High confidence	235.296	247.673	1.0526
726	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]	DDX39	Low confidence	192.552	187.412	1.02743
	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	FTSJ3	High confidence	244.495	232.419	1.05196
727	actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]	ARPC1A	Low confidence	201.571	196.189	1.02743
	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	NUAK1	High confidence	208.873	219.71	1.05188
728	igf-ii mrna-binding protein 2. [refseq;acc:nm_006548]	IGF2BP2	Low confidence	205.561	200.075	1.02742
	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505]	B3GNT1	High confidence	208.874	219.708	1.05187
729	28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	MRPS16	Low confidence	205.65	200.165	1.0274
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	no value	High confidence	208.874	219.708	1.05187
730	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	MRPS26	Low confidence	206.555	201.05	1.02738
	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]	TIMM10	High confidence	208.874	219.708	1.05187
731	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]	FH
	similar to trna synthetase class ii. [refseq;acc:nm_152268]	PARS2	Low confidence	203.316	197.904	1.02735
732	protein phosphatase 1, regulatory (inhibitor) subunit 5; phosphatase 1, regulatory inhibitor subunit 5. [refseq;acc:nm_005398]	PPP1R3C		203.592	198.172
	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	SEPT8	High confidence	124.434	118.318	1.05169
733	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	ACADVL		164	155.961	1.05154
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	MKI67IP	Low confidence	204.098	198.67	1.02732
734	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	no value	High confidence	232.601	244.534	1.0513
	septin 10 isoform 1. [refseq;acc:nm_144710]	SEPT10	Low confidence	153.764	149.678	1.0273
735	dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858]	LIG1		204.123	198.699
	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]	RANP1	High confidence	232.601	244.534	1.0513
736	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	no value
	rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690]	PDCD11	Low confidence	202.639	197.261	1.02726
737	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480]	OTC		179.918	175.156	1.02719
	septin 10 isoform 1. [refseq;acc:nm_144710]	SEPT10	High confidence	125.526	119.402	1.05129
738	epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204]	EPS8L1	Low confidence	206.474	201.013	1.02717
	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	XAB2	High confidence	222.825	211.966	1.05123
739	lysophospholipase 3 (lysosomal phospholipase a2); lcat-like lysophospholipase; likely ortholog of bovine lysosomal phospholipase a2; 1-o-acylceramide synthase; lysosomal phospholipase a2; lysophospholipase 3. [refseq;acc:nm_012320]	LYPLA3	Low confidence	204.348	198.945	1.02716
	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067]	PFAS	High confidence	223.58	235.027	1.0512
740	bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]	ATIC

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.