MK5 Microarray Data

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

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Showing element 1 to 50 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	red	description	green	network_comparison
1	UBAC1	10	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	2.4
2	no value	15	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). [swissprot;acc:o60476]	28	1.86667
3	PSCD1		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
4	PSCD2		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]
5	PSCD4		cytohesin 4. [swissprot;acc:q9uia0]
6	PSCD3		cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
7	HLX	215	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	1.49767
8	HBS1L		hbs1-like. [refseq;acc:nm_006620]
9	XAB1	212	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	309	1.45755
10	ATPBD1C		protein x 0004. [refseq;acc:nm_016301]
11	RINT1	337	rad50-interacting protein 1. [refseq;acc:nm_021930]	232	1.45259
12	RHOBTB2		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
13	UFC1	288.754	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	212.554	1.3585
14	ATG4A	56.6768	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	75.3531	1.32952
15	MAP1LC3B	56.7244	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	75.3948	1.32914
16	MAP1LC3A	56.7252	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	75.3954	1.32913
17	ATG4B	56.7841	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	75.447	1.32866
18	GBE1	185.678	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	245.247	1.32082
19	PYGB		glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]
20	PYGL		glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]
21	MYO15A		myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
22	PYGM		glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
23	MRPS17	58	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	44	1.31818
24	PANK1		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
25	PANK2		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
26	PANK3		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
27	SLC25A43		mitochondrial solute carrier protein. [refseq;acc:nm_145305]
28	ATF3	201.949	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	153.671	1.31416
29	PPP2R2D	187.458	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	243.678	1.29991
30	no value	187.457	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). [swissprot;acc:q00007]
31	PPP2R2B	187.458	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). [swissprot;acc:q00005]	243.677	1.2999
32	PPP2R2C	187.462	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). [swissprot;acc:q9y2t4]	243.673	1.29985
33	PPP2R1B	188.688	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	242.742	1.28647
34	PPP2R1A	189.07	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). [swissprot;acc:p30153]	242.453	1.28235
35	NFYC	260.532	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). [swissprot;acc:q13952]	204.309	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). [swissprot;acc:p23511]
37	PPP1R14A	322	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	253	1.27273
38	MFAP4		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]
39	PPP1R14D		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]
40	FCN2		ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
41	no value		protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]
42	FOS	204.641	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	160.957	1.2714
43	no value		jun dimerization protein. [refseq;acc:nm_130469]
44	FOSL2		fos-related antigen 2. [swissprot;acc:p15408]	161.046	1.2707
45	FOSB		protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	161.051	1.27066
46	FOSL1	204.642	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	161.068	1.27053
47	TMEM132A	325.586	gbp protein isoform a. [refseq;acc:nm_017870]	256.492	1.26938
48	GABARAP	65.4586	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	83.0461	1.26868
49	ARRB2	133	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	105	1.26667
50	ARRB1		beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.