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	network_comparison	green

Results: HTML CSV LaTeX

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	network_comparison	green
2163	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	3569.06	1.05213	3392.22
2164	ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9]	6952.66	1.05212	7315.06
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	1.05207	3461.4
2168	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8]	4561.75	1.05206	4799.24
2169	60s ribosomal protein l5. [swissprot;acc:p46777]	3639.65	1.05203	3459.64
2170	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	5825.61	1.05169	6126.74
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	1.05153	3462.96
2174	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	3641.45	1.05152	3463.02
2175	60s ribosomal protein l23a. [swissprot;acc:p29316]	3642.13	1.05146	3463.88
2176	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	6674.58	1.05114	7015.93
2177	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	5887.43	1.05102	6187.82
2178	elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717]	5893.23	1.05092	6193.33
2179	elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378]	5896.51	1.05089	6196.59
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	1.05084	6200.24
2181	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	4915.05	1.0508	5164.75
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	1.05077	6173.41
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	1.05042	6132.35
2185	60s ribosomal protein l12. [swissprot;acc:p30050]	3586.32	1.05035	3414.42
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	1.05022	7018.29
2189	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	5285.03	1.04996	5033.55
2190	phosducin-like protein (phlp). [swissprot;acc:q13371]	5285.38	1.04976	5034.86
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	1.04967	6504.93
2196	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	6688.64	1.04954	7020.02
2197	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	5285.79	1.04952	5036.39
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	1.04944	6657.98
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	1.04916	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	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235]	5259.97	1.0491	5518.26
2209	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076]	5259.1	1.04908	5517.22
2210	neurocalcin delta. [swissprot;acc:p29554]	5258.96		5517.06
2211	40s ribosomal protein s20. [swissprot;acc:p17075]	3590.56	1.04907	3422.6
2212	thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755]	6087.68	1.04898	6385.84

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.