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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Gene Rank Filtered description Network Comparison Type Value Type Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 51 to 100 of 3730 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence

Rank	Filtered	description	red	network_comparison	green	
26	0	dystrobrevin binding protein 1; dysbindin. [source:refseq;acc:nm_032122]	12128.3	1.60995	7533.33	
26	1	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	58	1.31818	44	
27	0	ptd016 protein. [source:refseq;acc:nm_016125]	18050	1.60673	11234	
27	1	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	58	1.31818	44	
28	0	p28 ing5. [source:refseq;acc:nm_032329]	12124.8	1.60337	7562.05	
28	1	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	201.949	1.31416	153.671	
29	0	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [source:swissprot;acc:p11086]	7395	1.57201	11625	
29	1	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	187.458	1.29991	243.678	
30	0	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [source:refseq;acc:nm_031938]	7395	1.57201	11625	
30	1	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]	187.457	1.29991	243.678	
31	0	leucine rich repeat (in flii) interacting protein 1. [source:refseq;acc:nm_004735]	8082.33	1.53462	5266.67	
31	1	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]	187.458	1.2999	243.677	
32	0	importin 9. [source:refseq;acc:nm_018085]	13292.2	1.52929	8691.76	
32	1	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]	187.462	1.29985	243.673	
33	0	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	13292.2	1.52929	8691.76	
33	1	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]	188.688	1.28647	242.742	
34	0	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [source:refseq;acc:nm_014268]	11284	1.52196	17173.8	
34	1	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]	189.07	1.28235	242.453	
35	0	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	3208.8	1.5182	4871.6	
35	1	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]	260.532	1.27519	204.309	
36	0	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	22422	1.4984	14964	
36	1	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]	260.532	1.27519	204.309	
37	0	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [source:sptrembl;acc:q9uge0]	3859	1.49458	2582	
37	1	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	322	1.27273	253	
38	0	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [source:swissprot;acc:p49336]	7230	1.48976	10771	
38	1	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	322	1.27273	253	
39	0	ero1-like. [source:refseq;acc:nm_014584]	13853	1.48242	20536	
39	1	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	322	1.27273	253	
40	0	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	3845	1.48218	5699	
40	1	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]	322	1.27273	253	
41	0	60s ribosomal protein l21. [source:swissprot;acc:p46778]	9994.33	1.47871	6758.83	
41	1	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]	322	1.27273	253	
42	0	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	8158	1.47509	5530.5	
42	1	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	204.641	1.2714	160.957	
43	0	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	12143.8	1.4533	8356.02	
43	1	jun dimerization protein. [source:refseq;acc:nm_130469]	204.641	1.2714	160.957	
44	0	serpin b12. [source:swissprot;acc:q96p63]	14604.2	1.44743	21138.6	
44	1	fos-related antigen 2. [source:swissprot;acc:p15408]	204.641	1.2707	161.046	
45	0	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	14592	1.44694	21113.7	
45	1	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	204.641	1.27066	161.051	
46	0	60s ribosomal protein l37a. [source:swissprot;acc:p12751]	12941.7	1.42943	18499.2	
46	1	fos-related antigen 1 (fra-1). [source:swissprot;acc:p15407]	204.642	1.27053	161.068	
47	0	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	12941.7	1.42943	18499.2	
47	1	gbp protein isoform a. [source:refseq;acc:nm_017870]	325.586	1.26938	256.492	
48	0	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [source:swissprot;acc:q16718]	9830	1.42278	6909	
48	1	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	65.4586	1.26868	83.0461	
49	0	brain protein 16. [source:refseq;acc:nm_016458]	6890.54	1.41927	4854.99	
49	1	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	133	1.26667	105	
50	0	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	9249.73	1.41533	13091.4	
50	1	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	133	1.26667	105	

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/