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 2201 to 2250 of 3228 in total

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

Rank	description	red	green	network_comparison
2201	cytochrome c. [swissprot;acc:p00001]	5076.73	5326.29	1.04916
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	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235]	5259.97	5518.26	1.0491
2209	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076]	5259.1	5517.22	1.04908
2210	neurocalcin delta. [swissprot;acc:p29554]	5258.96	5517.06
2211	40s ribosomal protein s20. [swissprot;acc:p17075]	3590.56	3422.6	1.04907
2212	thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755]	6087.68	6385.84	1.04898
2213	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]	6642.32	6967.61	1.04897
2214	chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]	5910.12	6199.28	1.04893
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	wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	6628.99	6952.04	1.04873
2219	arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7]	5853.67	6136.97	1.0484
2220	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	3936.2	3755.33	1.04816
2221	thrombospondin 3 precursor. [swissprot;acc:p49746]	3936.33	3755.5	1.04815
2222	sqv-7-like protein (fragment). [sptrembl;acc:o95454]	5309.65	5066.82	1.04793
2223	abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910]	5864.49	6145.14	1.04786
2224	quaking isoform 6. [sptrembl;acc:q9p0x9]
2225	60s ribosomal protein l9. [swissprot;acc:p32969]	3750.99	3580.35	1.04766
2226	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	3650.78	3484.91	1.0476
2227	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
2228	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	3650.82	3484.97	1.04759
2229	surfeit locus protein 5. [swissprot;acc:q15528]	3650.8	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	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	3614.08	3450.07	1.04754
2234	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	3614.07
2235	40s ribosomal protein s3. [swissprot;acc:p23396]	3674.29	3508.13	1.04736
2236	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023]	5902.27	6181.21	1.04726
2237	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911]	5902.26
2238	cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]	5902.27
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	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	3670.45	3504.91	1.04723
2242	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
2243	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	5776.96	6049.61	1.0472
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	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	6209.77	6501.99	1.04706
2247	rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062]	5819.36	6092.93	1.04701
2248	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	5833.01	6106.48	1.04688
2249	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	6834.03	7153.66	1.04677
2250	esterase d (ec 3.1.1.1). [swissprot;acc:p10768]

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.