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 2163 to 2212 of 3228 in total

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

Rank	description	red	green	network_comparison
2163	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	3569.06	3392.22	1.05213
2164	ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9]	6952.66	7315.06	1.05212
2165	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]
2166	squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534]
2167	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	3641.62	3461.4	1.05207
2168	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8]	4561.75	4799.24	1.05206
2169	60s ribosomal protein l5. [swissprot;acc:p46777]	3639.65	3459.64	1.05203
2170	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	5825.61	6126.74	1.05169
2171	phd finger protein 9. [refseq;acc:nm_018062]
2172	small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
2173	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	3641.4	3462.96	1.05153
2174	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	3641.45	3463.02	1.05152
2175	60s ribosomal protein l23a. [swissprot;acc:p29316]	3642.13	3463.88	1.05146
2176	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	6674.58	7015.93	1.05114
2177	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	5887.43	6187.82	1.05102
2178	elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717]	5893.23	6193.33	1.05092
2179	elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378]	5896.51	6196.59	1.05089
2180	elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926]	5900.25	6200.24	1.05084
2181	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	4915.05	5164.75	1.0508
2182	cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879]	5875.13	6173.41	1.05077
2183	cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561]	5875.11	6173.39
2184	rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9]	5838.01	6132.35	1.05042
2185	60s ribosomal protein l12. [swissprot;acc:p30050]	3586.32	3414.42	1.05035
2186	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	3586.3	3414.4
2187	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	3586.31	3414.41
2188	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	6682.7	7018.29	1.05022
2189	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	5285.03	5033.55	1.04996
2190	phosducin-like protein (phlp). [swissprot;acc:q13371]	5285.38	5034.86	1.04976
2191	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]
2192	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]
2193	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]
2194	dna repair protein rad52 homolog. [swissprot;acc:p43351]
2195	ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247]	6197.11	6504.93	1.04967
2196	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	6688.64	7020.02	1.04954
2197	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	5285.79	5036.39	1.04952
2198	complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021]	6344.31	6657.98	1.04944
2199	sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238]
2200	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]	5076.73	5326.29	1.04916
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	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

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.