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

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Showing element 2501 to 2550 of 3228 in total

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

red	green	Rank	description	network_comparison
6362.48	6647.42	2320	t54 protein. [swissprot;acc:q92917]	1.04478
6362.64	6976.1	984	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287]	1.09642
		985	integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]
		986	integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]
6362.92	6838.6	1495	nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000]	1.07476
6364.01	6819.38	1590	fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281]	1.07155
		1591	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155]
6365.03	6424.56	2648	tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399]	1.00935
6373.94	6666.87	2269	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853]	1.04596
6374.64	6667.06	2273	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	1.04587
6374.65	7145.59	662	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	1.12094
		663	tubby protein homolog. [swissprot;acc:p50607]
		664	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]
		665	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]
		666	tbc1 domain family member 5. [swissprot;acc:q92609]
		667	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]
		668	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]
		669	numb-like protein (numb-r). [swissprot;acc:q9y6r0]
		670	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]
		671	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
		672	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
6376.12	6833.59	1580	glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976]	1.07175
		1581	adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263]
		1582	protein x 0001. [refseq;acc:nm_016302]
		1583	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]
6380.32	6475.92	2616	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830]	1.01498
6380.6	6476.18	2608	trap/mediator complex component trap25. [refseq;acc:nm_080651]
		2611	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]
		2613	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]
6380.61	6476.19	2607	stromal interaction molecule 1 precursor. [swissprot;acc:q13586]
		2610	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]
		2612	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]
		2614	stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]
		2615	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]
6380.84	6476.41	2609	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]
6390.28	6973.08	1089	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549]	1.0912
6393.81	6984.94	1065	dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695]	1.09245
6399.54	6818.17	1807	endothelial-derived gene 1. [refseq;acc:nm_025205]	1.06542
6410.73	6962.22	1210	trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6]	1.08603
		1211	gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
6413.32	6941.48	1284	xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	1.08235
6416.68	7865.15	247	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	1.22574
6417.18	7859.59	249	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	1.22477
		253	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]
	7859.6	248	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]
		250	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
		251	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]
		252	crk-like protein. [swissprot;acc:p46109]
		254	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]
		255	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]

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.