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 Hugo 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	Hugo	description	green	red	network_comparison	
1	UBAC1	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	PSCD1	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	28	15	1.86667	
4	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	28	15	1.86667	
5	PSCD4	cytohesin 4. [source:swissprot;acc:q9uia0]	28	15	1.86667	
6	PSCD3	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	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	322	215	1.49767	
8	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	322	215	1.49767	
9	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	309	212	1.45755	
10	ATPBD1C	protein x 0004. [source:refseq;acc:nm_016301]	309	212	1.45755	
11	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	232	337	1.45259	
12	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	232	337	1.45259	
13	UFC1	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	212.554	288.754	1.3585	
14	ATG4A	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	MAP1LC3B	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	MAP1LC3A	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	ATG4B	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	75.447	56.7841	1.32866	
18	GBE1	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	PYGB	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	245.247	185.678	1.32082	
20	PYGL	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	245.247	185.678	1.32082	
21	MYO15A	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	245.247	185.678	1.32082	
22	PYGM	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	245.247	185.678	1.32082	
23	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	44	58	1.31818	
24	PANK1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	44	58	1.31818	
25	PANK2	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	44	58	1.31818	
26	PANK3	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	44	58	1.31818	
27	SLC25A43	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	44	58	1.31818	
28	ATF3	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	153.671	201.949	1.31416	
29	PPP2R2D	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	PPP2R2B	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	PPP2R2C	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	PPP2R1B	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	PPP2R1A	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	NFYC	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	NFYA	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	PPP1R14A	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	MFAP4	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	253	322	1.27273	
39	PPP1R14D	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	253	322	1.27273	
40	FCN2	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	FOS	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	FOSL2	fos-related antigen 2. [source:swissprot;acc:p15408]	161.046	204.641	1.2707	
45	FOSB	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	161.051	204.641	1.27066	
46	FOSL1	fos-related antigen 1 (fra-1). [source:swissprot;acc:p15407]	161.068	204.642	1.27053	
47	TMEM132A	gbp protein isoform a. [source:refseq;acc:nm_017870]	256.492	325.586	1.26938	
48	GABARAP	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	83.0461	65.4586	1.26868	
49	ARRB2	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	105	133	1.26667	
50	ARRB1	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	105	133	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/