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 green red network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	green	red	network_comparison	
26	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Divided	44	58	1.31818	
26	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	Subtracted	253	322	69	
27	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Subtracted	336.077	267.136	68.941	
27	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Divided	44	58	1.31818	
28	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Divided	153.671	201.949	1.31416	
28	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Subtracted	336.077	267.136	68.941	
29	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	Subtracted	336.075	267.139	68.936	
29	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Divided	243.678	187.458	1.29991	
30	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	Subtracted	336.075	267.14	68.935	
30	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [source:swissprot;acc:q00007]	Divided	243.678	187.457	1.29991	
31	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	Subtracted	336.075	267.14	68.935	
31	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [source:swissprot;acc:q00005]	Divided	243.677	187.458	1.2999	
32	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04899]	Subtracted	336.074	267.142	68.932	
32	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [source:swissprot;acc:q9y2t4]	Divided	243.673	187.462	1.29985	
33	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04898]	Subtracted	336.073	267.144	68.929	
33	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [source:swissprot;acc:p30154]	Divided	242.742	188.688	1.28647	
34	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [source:swissprot;acc:p08754]	Subtracted	336.073	267.144	68.929	
34	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [source:swissprot;acc:p30153]	Divided	242.453	189.07	1.28235	
35	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	Subtracted	335.359	267.636	67.723	
35	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Divided	204.309	260.532	1.27519	
36	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Divided	204.309	260.532	1.27519	
36	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Subtracted	254.434	320.927	66.493	
37	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	Subtracted	333.165	266.716	66.449	
37	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Divided	253	322	1.27273	
38	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Subtracted	333.281	266.933	66.348	
38	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Divided	253	322	1.27273	
39	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	Subtracted	334.483	268.565	65.918	
39	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Divided	253	322	1.27273	
40	deltex 2. [source:refseq;acc:nm_020892]	Subtracted	267.393	333.144	65.751	
40	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [source:swissprot;acc:q15485]	Divided	253	322	1.27273	
41	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Subtracted	267.274	332.925	65.651	
41	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	Divided	253	322	1.27273	
42	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	Divided	160.957	204.641	1.2714	
42	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Subtracted	267.246	332.874	65.628	
43	jun dimerization protein. [source:refseq;acc:nm_130469]	Divided	160.957	204.641	1.2714	
43	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Subtracted	267.246	332.874	65.628	
44	fos-related antigen 2. [source:swissprot;acc:p15408]	Divided	161.046	204.641	1.2707	
44	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Subtracted	267.246	332.874	65.628	
45	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Subtracted	267.246	332.874	65.628	
45	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	Divided	161.051	204.641	1.27066	
46	fos-related antigen 1 (fra-1). [source:swissprot;acc:p15407]	Divided	161.068	204.642	1.27053	
46	neuralized-like. [source:refseq;acc:nm_004210]	Subtracted	266.948	332.326	65.378	
47	gbp protein isoform a. [source:refseq;acc:nm_017870]	Divided	256.492	325.586	1.26938	
47	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Subtracted	290	350	60	
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Divided	83.0461	65.4586	1.26868	
48	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Subtracted	290	350	60	
49	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Divided	105	133	1.26667	
49	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Subtracted	290	350	60	
50	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Divided	105	133	1.26667	
50	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Subtracted	290	350	60	

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/