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.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 686 to 735 of 3228 in total

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

Rank	green	description	network_comparison	red
686	125.389	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.05602	132.413
687		retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]
688	250.823	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	1.05586	237.554
689	128.225	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	1.05579	135.379
690	208.987	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	1.05553	220.593
691	206.195	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	1.05532	217.602
692		cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]
693	234.847	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	1.05524	222.554
694	229.35	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	1.05475	241.907
695	214.405	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	1.05471	226.135
696	213.64	sr rich protein. [refseq;acc:nm_032870]	1.05455	225.293
697	209.113	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]	1.05419	220.444
698	209.118	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	1.05413	220.437
699		cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]		220.438
700		dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
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). [swissprot;acc:o14490]
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]	1.05411	232.468
712	209.123	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	1.05407	220.431
713	211.685	dendritic cell protein. [refseq;acc:nm_006360]	1.05402	223.121
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]	1.054	247.769
720	244.435	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	1.05396	231.92
721	203.8	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	1.0538	214.765
722	206.902	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	1.05341	217.952
723	232.577	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	1.05274	244.842
724		dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
725	247.673	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	1.0526	235.296
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]	1.05196	244.495
727	219.71	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	1.05188	208.873
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]	1.05187	208.874
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]	1.05169	124.434
733	155.961	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	1.05154	164
734	244.534	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	1.0513	232.601
735		gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]

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.