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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 2908 to 2957 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	red	green	network_comparison
727	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12]	Squared	25911.5	30281.9	1.16867
728	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	Measured	6000.23	6696.89	1.11611
	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]	Ranked	208.874	219.708	1.05187
	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	Rooted	59.7414	63.909	1.06976
	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281]	Squared	25911.8	30282.2	1.16866
729	exocyst complex component sec15a. [swissprot;acc:q8tag9]	Rooted	62.5069	66.8603	1.06965
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Ranked	208.874	219.708	1.05187
	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]	Measured	6000.23	6696.89	1.11611
	vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313]	Squared	25910.8	30280.9	1.16866
730	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]	Measured	6000.23	6696.89	1.11611
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Squared	24644.9	28800.7	1.16863
	exocyst complex component sec15b. [swissprot;acc:q9y2d4]	Rooted	62.5729	66.9286	1.06961
	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]	Ranked	208.874	219.708	1.05187
731	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Rooted	98.2298	91.8648	1.06929
	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]	Ranked	208.874	219.708	1.05187
	methyltransferase like 2. [refseq;acc:nm_018396]	Measured	13241.4	11864	1.1161
	vinculin (metavinculin). [swissprot;acc:p18206]	Squared	27463	32090.3	1.16849
732	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Measured	13241.4	11864	1.1161
	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	Rooted	51.8444	48.4963	1.06904
	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	Ranked	124.434	118.318	1.05169
	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487]	Squared	26029.8	30414.4	1.16845
733	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	Ranked	164	155.961	1.05154
	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Measured	13241.4	11864	1.1161
	nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	Rooted	52.0099	55.5904	1.06884
	vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488]	Squared	26029.1	30413.6	1.16845
734	loh1cr12. [refseq;acc:nm_058169]	Rooted	57.805	61.7803	1.06877
	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	Ranked	232.601	244.534	1.0513
	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Measured	13241.4	11864	1.1161
	vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050]	Squared	26032.5	30417.7	1.16845
735	atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632]		26030.5	30415.2	1.16844
	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]	Ranked	232.601	244.534	1.0513
	unr protein. [swissprot;acc:o75534]	Rooted	57.805	61.7803	1.06877
	vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449]	Measured	5768.32	6434.78	1.11554
736	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	Ranked	232.601	244.534	1.0513
	putative sialoglycoprotease type 2. [refseq;acc:nm_022353]	Squared	22017.1	25721.9	1.16827
	sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167]	Measured	5768.32	6434.78	1.11554
	wd-repeat protein 3. [swissprot;acc:q9unx4]	Rooted	51.5438	55.0853	1.06871
737	golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735]	Measured	5768.32	6434.78	1.11554
	pnas-18. [sptrembl;acc:q9bzu3]	Rooted	97.8205	91.5467	1.06853
	septin 10 isoform 1. [refseq;acc:nm_144710]	Ranked	125.526	119.402	1.05129
	transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725]	Squared	31479.4	36770.8	1.16809
738	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629]	Measured	5768.32	6434.78	1.11554
	syntaxin 7. [swissprot;acc:o15400]	Rooted	61.5022	65.7076	1.06838
	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	Squared	31467.1	36752.2	1.16796
	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	Ranked	222.825	211.966	1.05123
739	cellular modulator of immune recognition. [refseq;acc:nm_145021]	Measured	5768.32	6434.78	1.11554
	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	Rooted	65.3677	69.828	1.06823
	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067]	Ranked	223.58	235.027	1.0512
	ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792]	Squared	25727.7	30046.7	1.16787
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]	Ranked	223.58	235.027	1.0512

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
- 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.