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

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Showing element 613 to 662 of 3228 in total

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

Rank	description	red	green	network_comparison
613	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	3975.77	4485.05	1.1281
614	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	11222.2	9948.93	1.12798
615	cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
616	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]
617	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	5162.52	5822.47	1.12783
618	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	7878.27	8879.08	1.12703
619	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	3879.99	4371.24	1.12661
620	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]	6227.87	7012.9	1.12605
621	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	4115.39	4633.96	1.12601
622	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	6228.42	7013.21	1.126
623	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	6228.39	7013.19
624	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
625	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]
626	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]
627	limkain b1. [refseq;acc:nm_019081]
628	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
629	cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]
630	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]
631	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042]
632	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
633	ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]
634	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
635	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	6228.97	7013.53	1.12595
636	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066]	5713.41	6432.92	1.12593
637	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	7756.51	8731.76	1.12573
638	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531]	7755.69	8730.74	1.12572
639	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392]	7753.59	8728.13	1.12569
640	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	4811.02	5414.64	1.12547
641	peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911]	4810.85	5414.21	1.12542
642	atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]		5414.23
643	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025]
644	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]		5414.22
645	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711]	4810.71	5413.89	1.12538
646	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	4019.88	4522.61	1.12506
647	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	5167.88	4594.43	1.12481
648	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	5248.07	5901.72	1.12455
649	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]
650	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	8362.81	9402.7	1.12435
651	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	5168.43	4597.44	1.1242
652	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
653	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	5560.06	6248.27	1.12378
654	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	4088.63	4593.43	1.12346
655	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
656	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	6139.04	6893.7	1.12293
657	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	6079.26	6824.47	1.12258
658	apical-like protein (apxl protein). [swissprot;acc:q13796]	6088.77	6834.87	1.12254
659	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	6089.21	6835.34	1.12253
660	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	5575.18	6254.85	1.12191
661	step ii splicing factor slu7. [refseq;acc:nm_006425]
662	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	6374.65	7145.59	1.12094

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.