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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

Results: HTML CSV LaTeX

Showing element 701 to 750 of 3228 in total

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

Rank	green	description	red	network_comparison
701	209.118	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]	220.438	1.05413
702		putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]
703		limkain b1. [refseq;acc:nm_019081]
704		putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
705		cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]
706		disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]
707		kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042]
708		disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
709		ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]
710		disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
711	245.048	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	232.468	1.05411
712	209.123	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	220.431	1.05407
713	211.685	dendritic cell protein. [refseq;acc:nm_006360]	223.121	1.05402
714		potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]
715		carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
716		cpz gene product. [refseq;acc:nm_003652]
717		carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]
718		potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]
719	235.074	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	247.769	1.054
720	244.435	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	231.92	1.05396
721	203.8	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	214.765	1.0538
722	206.902	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	217.952	1.05341
723	232.577	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	244.842	1.05274
724		dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
725	247.673	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	235.296	1.0526
726	232.419	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	244.495	1.05196
727	219.71	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	208.873	1.05188
728	219.708	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]	208.874	1.05187
729		huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]
730		mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]
731		fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]
732	118.318	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	124.434	1.05169
733	155.961	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	164	1.05154
734	244.534	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	232.601	1.0513
735		gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]
736		presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
737	119.402	septin 10 isoform 1. [refseq;acc:nm_144710]	125.526	1.05129
738	211.966	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	222.825	1.05123
739	235.027	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067]	223.58	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]
741		multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234]
742	120.078	brain protein 44. [swissprot;acc:o95563]	126.215	1.05111
743		septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]
744	120.463	septin 6. [swissprot;acc:q14141]	126.604	1.05098
745	225.568	solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827]	214.679	1.05072
746	238.38	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]	250.465	1.0507
747		trinucleotide repeat containing 15. [refseq;acc:nm_015575]
748	233.483	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	245.246	1.05038
749	211.326	exocyst complex component sec15b. [swissprot;acc:q9y2d4]	221.968	1.05036
750	211.503	exocyst complex component sec15a. [swissprot;acc:q8tag9]	222.138	1.05028

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.