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

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Showing element 2200 to 2249 of 3228 in total

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

Rank	network_comparison	red	description	green
2200	1.04916	5076.73	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]	5326.29
2201			cytochrome c. [swissprot;acc:p00001]
2202			heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]
2203			heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807]
2204			fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306]
2205			ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312]
2206			elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
2207			rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756]
2208	1.0491	5259.97	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235]	5518.26
2209	1.04908	5259.1	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076]	5517.22
2210		5258.96	neurocalcin delta. [swissprot;acc:p29554]	5517.06
2211	1.04907	3590.56	40s ribosomal protein s20. [swissprot;acc:p17075]	3422.6
2212	1.04898	6087.68	thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755]	6385.84
2213	1.04897	6642.32	proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618]	6967.61
2214	1.04893	5910.12	chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]	6199.28
2215			kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9]
2216			conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]
2217			kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]
2218	1.04873	6628.99	wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	6952.04
2219	1.0484	5853.67	arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7]	6136.97
2220	1.04816	3936.2	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	3755.33
2221	1.04815	3936.33	thrombospondin 3 precursor. [swissprot;acc:p49746]	3755.5
2222	1.04793	5309.65	sqv-7-like protein (fragment). [sptrembl;acc:o95454]	5066.82
2223	1.04786	5864.49	abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910]	6145.14
2224			quaking isoform 6. [sptrembl;acc:q9p0x9]
2225	1.04766	3750.99	60s ribosomal protein l9. [swissprot;acc:p32969]	3580.35
2226	1.0476	3650.78	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	3484.91
2227			gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
2228	1.04759	3650.82	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	3484.97
2229		3650.8	surfeit locus protein 5. [swissprot;acc:q15528]	3484.94
2230			zinc finger protein 291. [swissprot;acc:q9by12]
2231			peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]
2232			protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]
2233	1.04754	3614.08	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	3450.07
2234		3614.07	ribosomal protein l10-like protein. [refseq;acc:nm_080746]
2235	1.04736	3674.29	40s ribosomal protein s3. [swissprot;acc:p23396]	3508.13
2236	1.04726	5902.27	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023]	6181.21
2237		5902.26	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911]
2238		5902.27	cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]
2239			sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637]
2240			sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]
2241	1.04723	3670.45	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	3504.91
2242			40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
2243	1.0472	5776.96	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	6049.61
2244			gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915]
2245			inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839]
2246	1.04706	6209.77	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	6501.99
2247	1.04701	5819.36	rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062]	6092.93
2248	1.04688	5833.01	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	6106.48
2249	1.04677	6834.03	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	7153.66

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.