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

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Showing element 982 to 1031 of 3228 in total

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

green	Rank	description	red	network_comparison
5131.89	1656	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]	5488.7	1.06953
	1657	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
	1659	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]
5132.35	1611	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	5497.73	1.07119
5145.39	2263	40s ribosomal protein s3a. [swissprot;acc:p49241]	4918.64	1.0461
5154.43	2695	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	5176.92	1.00436
	2696	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]
	2697	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]
5155.87	2457	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	4998.72	1.03144
5158.86	1332	my016 protein. [sptrembl;acc:q9h3k6]	4775.25	1.08033
5164.75	2181	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	4915.05	1.0508
5187.78	2557	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	5291.65	1.02002
	2558	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
	2559	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]
	2560	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
	2561	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]
	2562	cgthba protein (-14 gene protein). [swissprot;acc:q12980]
	2563	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]
5192.61	261	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	4247.36	1.22255
5193.42	260		4244.95	1.22343
5197.18	2730	myelin gene expression factor 2. [refseq;acc:nm_016132]	5214.9	1.00341
5198.91	1044	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	4757.46	1.09279
	1046	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]
	1047	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]
	1048	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
	1049	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
	1050	neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
	1051	homeobox protein dlx-2. [swissprot;acc:q07687]
	1052	homeobox protein dlx-5. [swissprot;acc:p56178]
	1053	fetal brain protein 239 (239fb). [swissprot;acc:q15777]
	1054	homeobox protein dlx-3. [swissprot;acc:o60479]
	1055	activated p21cdc42hs kinase. [refseq;acc:nm_005781]
	1056	mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]
5208.98	243	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	4246.95	1.22652
5211.25	244	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	4250.14	1.22614
5212.33	245	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	4251.65	1.22595
5213.05	246	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	4252.66	1.22583
5222.25	393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	4490.28	1.16301
	394	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]
5223.69	2009	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	4934.48	1.05861
5223.95	416	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	4509.54	1.15842
5224.27	2020	diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384]	4935.84	1.05844
5226.71	805	60s ribosomal protein l39. [swissprot;acc:p02404]	4708.61	1.11003
	806	60s ribosomal protein l18a. [swissprot;acc:q02543]
	807	40s ribosomal protein s19. [swissprot;acc:p39019]
	808	60s ribosomal protein l31. [swissprot;acc:p12947]
5233.14	417	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	4522.71	1.15708
5237.77	873	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	4749.52	1.1028
5243.23	1244	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	4835.55	1.08431
	1245	casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]

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.