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

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Showing element 682 to 731 of 3228 in total

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

Rank	description	green	red	network_comparison
682	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	125.389	132.413	1.05602
683	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]
684	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
685	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]
686	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
687	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]
688	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	250.823	237.554	1.05586
689	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	128.225	135.379	1.05579
690	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	208.987	220.593	1.05553
691	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	206.195	217.602	1.05532
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	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]	234.847	222.554	1.05524
694	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	229.35	241.907	1.05475
695	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	214.405	226.135	1.05471
696	sr rich protein. [refseq;acc:nm_032870]	213.64	225.293	1.05455
697	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]	209.113	220.444	1.05419
698	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	209.118	220.437	1.05413
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	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	245.048	232.468	1.05411
712	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	209.123	220.431	1.05407
713	dendritic cell protein. [refseq;acc:nm_006360]	211.685	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	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	235.074	247.769	1.054
720	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	244.435	231.92	1.05396
721	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	203.8	214.765	1.0538
722	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	206.902	217.952	1.05341
723	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	232.577	244.842	1.05274
724	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
725	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	247.673	235.296	1.0526
726	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	232.419	244.495	1.05196
727	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	219.71	208.873	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). [swissprot;acc:o43505]	219.708	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]

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.