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

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Showing element 680 to 729 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
680	HOXB4	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	132.413	125.389	1.05602
681	HOXC5	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]
682	no value	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
683	HOXD4	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]
684	HOXB5	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
685	HOXA5	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]
686	no value	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
687	HSD17B14	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]
688	POLR2D	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	237.554	250.823	1.05586
689	TCP1	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	135.379	128.225	1.05579
690	SNW1	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	220.593	208.987	1.05553
691	BCAS2	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	217.602	206.195	1.05532
692	CDC5L	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	NOVA1	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]	222.554	234.847	1.05524
694	POLE	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	241.907	229.35	1.05475
695	PPIL4	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	226.135	214.405	1.05471
696	SFRS18	sr rich protein. [refseq;acc:nm_032870]	225.293	213.64	1.05455
697	FTH1	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]	220.444	209.113	1.05419
698	FTMT	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	220.437	209.118	1.05413
699	CREG2	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	220.438
700	no value	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
701	DLGAP1	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	AHCYL1	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]
703	KIAA0430	limkain b1. [refseq;acc:nm_019081]
704	no value	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
705	CREG1	cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]
706	DLGAP3	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	KNG1	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042]
708	no value	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	FTL	ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]
710	DLGAP4	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
711	YARS	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	232.468	245.048	1.05411
712	FTHL17	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	220.431	209.123	1.05407
713	EIF3M	dendritic cell protein. [refseq;acc:nm_006360]	223.121	211.685	1.05402
714	CPXM2	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]
715	CPN1	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	cpz gene product. [refseq;acc:nm_003652]
717	CPE	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]
718	CPXM1	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]
719	NOL5A	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	247.769	235.074	1.054
720	RPLP2	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	231.92	244.435	1.05396
721	EXOC5	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	214.765	203.8	1.0538
722	TREH	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	217.952	206.902	1.05341
723	no value	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	244.842	232.577	1.05274
724		dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
725	MVK	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	235.296	247.673	1.0526
726	FTSJ3	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	232.419	1.05196
727	NUAK1	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	208.873	219.71	1.05188
728	B3GNT1	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	219.708	1.05187
729	no value	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]

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
- Hugo is the HGNC identifier if it exists
- 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.