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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 8289 in total

Network Comparison Type	Divided
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Interaction Map	red	green	network_comparison	
1	CPD	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Low confidence	16	32	2	
1	UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	High confidence	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]	High confidence	15	28	1.86667	
2	LAMP1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	223	330	1.47982	
3	CDK4	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	223	330	1.47982	
3	PSCD1	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	High confidence	15	28	1.86667	
4	CDK6	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	223	330	1.47982	
4	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	High confidence	15	28	1.86667	
5	LAMP2	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	223	330	1.47982	
5	PSCD4	cytohesin 4. [source:swissprot;acc:q9uia0]	High confidence	15	28	1.86667	
6	OSBPL6	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	318	240	1.325	
6	PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	High confidence	15	28	1.86667	
7	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	215	322	1.49767	
7	OSBPL3	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	318	240	1.325	
8	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	215	322	1.49767	
8	OSBPL7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Low confidence	318	240	1.325	
9	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Low confidence	58	44	1.31818	
9	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	High confidence	212	309	1.45755	
10	ATPBD1C	protein x 0004. [source:refseq;acc:nm_016301]	High confidence	212	309	1.45755	
10	SLC25A43	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Low confidence	58	44	1.31818	
11	BEST1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [source:swissprot;acc:o76090]	Low confidence	37.318	28.4944	1.30966	
11	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	337	232	1.45259	
12	BEST4	vitelliform macular dystrophy 2-like protein 2. [source:refseq;acc:nm_153274]	Low confidence	37.3475	28.5242	1.30933	
12	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	337	232	1.45259	
13		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Low confidence	37.9984	29.1831	1.30207	
13	UFC1	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	High confidence	288.754	212.554	1.3585	
14	ATG4A	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	High confidence	56.6768	75.3531	1.32952	
14	BEST2	vitelliform macular dystrophy 2-like protein 1. [source:refseq;acc:nm_017682]	Low confidence	37.9984	29.1831	1.30207	
15	MAP1LC3B	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	High confidence	56.7244	75.3948	1.32914	
15	UFC1	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Low confidence	255.046	202.362	1.26035	
16	JMJD1C	thyroid receptor interacting protein 8 (trip-8) (fragment). [source:swissprot;acc:q15652]	Low confidence	305.472	247.246	1.2355	
16	MAP1LC3A	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	High confidence	56.7252	75.3954	1.32913	
17	ATG4B	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	High confidence	56.7841	75.447	1.32866	
17	TMEM132A	gbp protein isoform a. [source:refseq;acc:nm_017870]	Low confidence	305.399	247.213	1.23537	
18	GBE1	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	High confidence	185.678	245.247	1.32082	
18	JMJD1A	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [source:refseq;acc:nm_018433]	Low confidence	305.303	247.169	1.2352	
19	PRSS3	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [source:swissprot;acc:p35030]	Low confidence	304.548	246.824	1.23387	
19	PYGB	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	High confidence	185.678	245.247	1.32082	
20	PRSS1	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [source:swissprot;acc:p07477]	Low confidence	304.359	246.737	1.23354	
20	PYGL	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	High confidence	185.678	245.247	1.32082	
21	MYO15A	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	High confidence	185.678	245.247	1.32082	
21	PIGF	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [source:swissprot;acc:q07326]	Low confidence	198	163	1.21472	
22	PYGM	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	High confidence	185.678	245.247	1.32082	
22	TUSC3	n33 protein. [source:swissprot;acc:q13454]	Low confidence	198	163	1.21472	
23		implantation-associated protein. [source:refseq;acc:nm_032121]	Low confidence	198	163	1.21472	
23	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	High confidence	58	44	1.31818	
24	HINT1	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [source:swissprot;acc:p49773]	Low confidence	188.298	228.509	1.21355	
24	PANK1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	High confidence	58	44	1.31818	
25	CYP27B1	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	Low confidence	286.396	238.476	1.20094	
25	PANK2	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	High confidence	58	44	1.31818	

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/