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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Hugo Value Type Network Comparison Type Interaction Map Filtered red green 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	Hugo	red	green	network_comparison	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	UBAC1	10	24	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]		15	28	1.86667	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	PSCD1	15	28	1.86667	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	PSCD2	15	28	1.86667	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	PSCD4	15	28	1.86667	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	PSCD3	15	28	1.86667	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	HLX	215	322	1.49767	
8	hbs1-like. [source:refseq;acc:nm_006620]	HBS1L	215	322	1.49767	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	XAB1	212	309	1.45755	
10	protein x 0004. [source:refseq;acc:nm_016301]	ATPBD1C	212	309	1.45755	
11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	RINT1	337	232	1.45259	
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	RHOBTB2	337	232	1.45259	
13	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	UFC1	288.754	212.554	1.3585	
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	ATG4A	56.6768	75.3531	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]	MAP1LC3B	56.7244	75.3948	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]	MAP1LC3A	56.7252	75.3954	1.32913	
17	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	ATG4B	56.7841	75.447	1.32866	
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	GBE1	185.678	245.247	1.32082	
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	PYGB	185.678	245.247	1.32082	
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	PYGL	185.678	245.247	1.32082	
21	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	MYO15A	185.678	245.247	1.32082	
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	PYGM	185.678	245.247	1.32082	
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	MRPS17	58	44	1.31818	
24	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	PANK1	58	44	1.31818	
25	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	PANK2	58	44	1.31818	
26	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	PANK3	58	44	1.31818	
27	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	SLC25A43	58	44	1.31818	
28	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	ATF3	201.949	153.671	1.31416	
29	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	PPP2R2D	187.458	243.678	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]		187.457	243.678	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]	PPP2R2B	187.458	243.677	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]	PPP2R2C	187.462	243.673	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]	PPP2R1B	188.688	242.742	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]	PPP2R1A	189.07	242.453	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]	NFYC	260.532	204.309	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]	NFYA	260.532	204.309	1.27519	
37	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	PPP1R14A	322	253	1.27273	
38	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	MFAP4	322	253	1.27273	
39	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	PPP1R14D	322	253	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]	FCN2	322	253	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]		322	253	1.27273	
42	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	FOS	204.641	160.957	1.2714	
43	jun dimerization protein. [source:refseq;acc:nm_130469]		204.641	160.957	1.2714	
44	fos-related antigen 2. [source:swissprot;acc:p15408]	FOSL2	204.641	161.046	1.2707	
45	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	FOSB	204.641	161.051	1.27066	
46	fos-related antigen 1 (fra-1). [source:swissprot;acc:p15407]	FOSL1	204.642	161.068	1.27053	
47	gbp protein isoform a. [source:refseq;acc:nm_017870]	TMEM132A	325.586	256.492	1.26938	
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	GABARAP	65.4586	83.0461	1.26868	
49	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	ARRB2	133	105	1.26667	
50	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	ARRB1	133	105	1.26667	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/