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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 701 to 750 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	red	green	network_comparison	
701	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). [source:swissprot;acc:o14490]	220.438	209.118	1.05413	
702	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	220.438	209.118	1.05413	
703	limkain b1. [source:refseq;acc:nm_019081]	220.438	209.118	1.05413	
704	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	220.438	209.118	1.05413	
705	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	220.438	209.118	1.05413	
706	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	220.438	209.118	1.05413	
707	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	220.438	209.118	1.05413	
708	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	220.438	209.118	1.05413	
709	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	220.438	209.118	1.05413	
710	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	220.438	209.118	1.05413	
711	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [source:swissprot;acc:p54577]	232.468	245.048	1.05411	
712	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	220.431	209.123	1.05407	
713	dendritic cell protein. [source:refseq;acc:nm_006360]	223.121	211.685	1.05402	
714	potential carboxypeptidase-like protein x2 precursor. [source:swissprot;acc:q8n436]	223.121	211.685	1.05402	
715	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [source:swissprot;acc:p15169]	223.121	211.685	1.05402	
716	cpz gene product. [source:refseq;acc:nm_003652]	223.121	211.685	1.05402	
717	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	223.121	211.685	1.05402	
718	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [source:swissprot;acc:q96sm3]	223.121	211.685	1.05402	
719	nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	247.769	235.074	1.054	
720	60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	231.92	244.435	1.05396	
721	exocyst complex component sec10 (hsec10). [source:swissprot;acc:o00471]	214.765	203.8	1.0538	
722	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [source:swissprot;acc:o43280]	217.952	206.902	1.05341	
723	histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	244.842	232.577	1.05274	
724	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	244.842	232.577	1.05274	
725	mevalonate kinase (ec 2.7.1.36) (mk). [source:swissprot;acc:q03426]	235.296	247.673	1.0526	
726	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	244.495	232.419	1.05196	
727	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [source:swissprot;acc:o60285]	208.873	219.71	1.05188	
728	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). [source:swissprot;acc:o43505]	208.874	219.708	1.05187	
729	huntingtin interacting protein e; huntingtin interactor protein e. [source:refseq;acc:nm_007076]	208.874	219.708	1.05187	
730	mitochondrial import inner membrane translocase subunit tim10. [source:swissprot;acc:q9y5j8]	208.874	219.708	1.05187	
731	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [source:swissprot;acc:p07954]	208.874	219.708	1.05187	
732	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	124.434	118.318	1.05169	
733	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	164	155.961	1.05154	
734	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [source:swissprot;acc:q8tct8]	232.601	244.534	1.0513	
735	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [source:swissprot;acc:p17080]	232.601	244.534	1.0513	
736	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	232.601	244.534	1.0513	
737	septin 10 isoform 1. [source:refseq;acc:nm_144710]	125.526	119.402	1.05129	
738	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	222.825	211.966	1.05123	
739	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [source:swissprot;acc:o15067]	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)]. [source:swissprot;acc:p31939]	223.58	235.027	1.0512	
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)]. [source:swissprot;acc:p22234]	223.58	235.027	1.0512	
742	brain protein 44. [source:swissprot;acc:o95563]	126.215	120.078	1.05111	
743	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	126.215	120.078	1.05111	
744	septin 6. [source:swissprot;acc:q14141]	126.604	120.463	1.05098	
745	solute carrier family 35, member b1; udp-galactose transporter related. [source:refseq;acc:nm_005827]	214.679	225.568	1.05072	
746	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	250.465	238.38	1.0507	
747	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	250.465	238.38	1.0507	
748	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	245.246	233.483	1.05038	
749	exocyst complex component sec15b. [source:swissprot;acc:q9y2d4]	221.968	211.326	1.05036	
750	exocyst complex component sec15a. [source:swissprot;acc:q8tag9]	222.138	211.503	1.05028	

Legend:
- Rank is the rank after comparing the two networks
- 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/