Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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
Results: HTML CSV LaTeX Showing element 2175 to 2224 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2175	60s ribosomal protein l23a. [source: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). [source: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). [source:swissprot;acc:q14576]	5887.43	6187.82	1.05102	
2178	elav-like protein 1 (hu-antigen r) (hur). [source:swissprot;acc:q15717]	5893.23	6193.33	1.05092	
2179	elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [source: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). [source:swissprot;acc:q12926]	5900.25	6200.24	1.05084	
2181	triosephosphate isomerase (ec 5.3.1.1) (tim). [source: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). [source: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. [source:refseq;acc:nm_006561]	5875.11	6173.39	1.05077	
2184	rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [source:swissprot;acc:q9h0z9]	5838.01	6132.35	1.05042	
2185	60s ribosomal protein l12. [source:swissprot;acc:p30050]	3586.32	3414.42	1.05035	
2186	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	3586.3	3414.4	1.05035	
2187	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	3586.31	3414.41	1.05035	
2188	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [source:swissprot;acc:q09470]	6682.7	7018.29	1.05022	
2189	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	5285.03	5033.55	1.04996	
2190	phosducin-like protein (phlp). [source: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). [source:swissprot;acc:p27694]	5285.38	5034.86	1.04976	
2192	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	5285.38	5034.86	1.04976	
2193	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	5285.38	5034.86	1.04976	
2194	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	5285.38	5034.86	1.04976	
2195	ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [source: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). [source:swissprot;acc:p22459]	6688.64	7020.02	1.04954	
2197	clathrin heavy chain 2 (clh-22). [source: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). [source: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). [source:refseq;acc:nm_012238]	6344.31	6657.98	1.04944	
2200	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [source:swissprot;acc:p98175]	5076.73	5326.29	1.04916	
2201	cytochrome c. [source:swissprot;acc:p00001]	5076.73	5326.29	1.04916	
2202	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	5076.73	5326.29	1.04916	
2203	heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [source:refseq;acc:nm_004807]	5076.73	5326.29	1.04916	
2204	fatty acid hydroxylase domain containing 1. [source:refseq;acc:nm_024306]	5076.73	5326.29	1.04916	
2205	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [source:refseq;acc:nm_016312]	5076.73	5326.29	1.04916	
2206	elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [source:refseq;acc:nm_018127]	5076.73	5326.29	1.04916	
2207	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [source:swissprot;acc:p52756]	5076.73	5326.29	1.04916	
2208	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [source:swissprot;acc:p37235]	5259.97	5518.26	1.0491	
2209	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [source:swissprot;acc:p32076]	5259.1	5517.22	1.04908	
2210	neurocalcin delta. [source:swissprot;acc:p29554]	5258.96	5517.06	1.04908	
2211	40s ribosomal protein s20. [source:swissprot;acc:p17075]	3590.56	3422.6	1.04907	
2212	thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [source: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). [source:swissprot;acc:p20618]	6642.32	6967.61	1.04897	
2214	chromosome 11 open reading frame2; chromosome  11 open reading frame2. [source:refseq;acc:nm_013265]	5910.12	6199.28	1.04893	
2215	kinesin-like protein kif13a (kinesin-like protein rbkin). [source:swissprot;acc:q9h1h9]	5910.12	6199.28	1.04893	
2216	conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [source:swissprot;acc:q14746]	5910.12	6199.28	1.04893	
2217	kinesin-like protein kif13b (kinesin-like protein gakin). [source:swissprot;acc:q9nqt8]	5910.12	6199.28	1.04893	
2218	wilms' tumor 1-associating protein (wt1-associated protein). [source:swissprot;acc:q15007]	6628.99	6952.04	1.04873	
2219	arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [source:swissprot;acc:q9y2x7]	5853.67	6136.97	1.0484	
2220	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	3936.2	3755.33	1.04816	
2221	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	3936.33	3755.5	1.04815	
2222	sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	5309.65	5066.82	1.04793	
2223	abhydrolase domain containing protein 2 (protein phps1-2). [source:swissprot;acc:p08910]	5864.49	6145.14	1.04786	
2224	quaking isoform 6. [source:sptrembl;acc:q9p0x9]	5864.49	6145.14	1.04786	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/