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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Filtered Rank Gene description Value Type Network Comparison Type Interaction Map red network_comparison green

Results: HTML CSV LaTeX

Showing element 501 to 550 of 3730 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Filtered	Rank	description	red	network_comparison	green	
0	501	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	0.00001	1	0.00001	
0	502	brca1 associated protein. [source:refseq;acc:nm_006768]	0.00001	1	0.00001	
1	1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	10	2.4	24	
1	2	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	15	1.86667	28	
1	3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	15	1.86667	28	
1	4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	15	1.86667	28	
1	5	cytohesin 4. [source:swissprot;acc:q9uia0]	15	1.86667	28	
1	6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	15	1.86667	28	
1	7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	215	1.49767	322	
1	8	hbs1-like. [source:refseq;acc:nm_006620]	215	1.49767	322	
1	9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	212	1.45755	309	
1	10	protein x 0004. [source:refseq;acc:nm_016301]	212	1.45755	309	
1	11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	337	1.45259	232	
1	12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	337	1.45259	232	
1	13	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	288.754	1.3585	212.554	
1	14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	56.6768	1.32952	75.3531	
1	15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	56.7244	1.32914	75.3948	
1	16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	56.7252	1.32913	75.3954	
1	17	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	56.7841	1.32866	75.447	
1	18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	185.678	1.32082	245.247	
1	19	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	185.678	1.32082	245.247	
1	20	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	185.678	1.32082	245.247	
1	21	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	185.678	1.32082	245.247	
1	22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	185.678	1.32082	245.247	
1	23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	58	1.31818	44	
1	24	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	58	1.31818	44	
1	25	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	58	1.31818	44	
1	26	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	58	1.31818	44	
1	27	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	58	1.31818	44	
1	28	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	201.949	1.31416	153.671	
1	29	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	187.458	1.29991	243.678	
1	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]	187.457	1.29991	243.678	
1	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]	187.458	1.2999	243.677	
1	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]	187.462	1.29985	243.673	
1	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]	188.688	1.28647	242.742	
1	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]	189.07	1.28235	242.453	
1	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]	260.532	1.27519	204.309	
1	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]	260.532	1.27519	204.309	
1	37	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	322	1.27273	253	
1	38	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	322	1.27273	253	
1	39	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	322	1.27273	253	
1	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]	322	1.27273	253	
1	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]	322	1.27273	253	
1	42	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	204.641	1.2714	160.957	
1	43	jun dimerization protein. [source:refseq;acc:nm_130469]	204.641	1.2714	160.957	
1	44	fos-related antigen 2. [source:swissprot;acc:p15408]	204.641	1.2707	161.046	
1	45	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	204.641	1.27066	161.051	
1	46	fos-related antigen 1 (fra-1). [source:swissprot;acc:p15407]	204.642	1.27053	161.068	
1	47	gbp protein isoform a. [source:refseq;acc:nm_017870]	325.586	1.26938	256.492	
1	48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	65.4586	1.26868	83.0461	

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/