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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
    Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	green	red	network_comparison	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	24	10	2.4	
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]	28	15	1.86667	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	28	15	1.86667	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	28	15	1.86667	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	28	15	1.86667	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	28	15	1.86667	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	322	215	1.49767	
8	hbs1-like. [source:refseq;acc:nm_006620]	322	215	1.49767	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	309	212	1.45755	
10	protein x 0004. [source:refseq;acc:nm_016301]	309	212	1.45755	
11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	232	337	1.45259	
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	232	337	1.45259	
13	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	212.554	288.754	1.3585	
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	75.3531	56.6768	1.32952	
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	75.3948	56.7244	1.32914	
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	75.3954	56.7252	1.32913	
17	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	75.447	56.7841	1.32866	
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	245.247	185.678	1.32082	
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	245.247	185.678	1.32082	
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	245.247	185.678	1.32082	
21	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	245.247	185.678	1.32082	
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	245.247	185.678	1.32082	
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	44	58	1.31818	
24	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	44	58	1.31818	
25	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	44	58	1.31818	
26	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	44	58	1.31818	
27	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	44	58	1.31818	
28	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	153.671	201.949	1.31416	
29	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	243.678	187.458	1.29991	
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]	243.678	187.457	1.29991	
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]	243.677	187.458	1.2999	
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]	243.673	187.462	1.29985	
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]	242.742	188.688	1.28647	
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]	242.453	189.07	1.28235	
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]	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]	204.309	260.532	1.27519	
37	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	253	322	1.27273	
38	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	253	322	1.27273	
39	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	253	322	1.27273	
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]	253	322	1.27273	
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]	253	322	1.27273	
42	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	160.957	204.641	1.2714	
43	jun dimerization protein. [source:refseq;acc:nm_130469]	160.957	204.641	1.2714	
44	fos-related antigen 2. [source:swissprot;acc:p15408]	161.046	204.641	1.2707	
45	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	161.051	204.641	1.27066	
46	fos-related antigen 1 (fra-1). [source:swissprot;acc:p15407]	161.068	204.642	1.27053	
47	gbp protein isoform a. [source:refseq;acc:nm_017870]	256.492	325.586	1.26938	
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	83.0461	65.4586	1.26868	
49	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	105	133	1.26667	
50	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	105	133	1.26667	

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/