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

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 3730 in total

Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence

Rank	description	Filtered	green	red	network_comparison	
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	0	15915	4294	3.70633	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	1	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]	1	28	15	1.86667	
2	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	0	14977	5865	2.55362	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	1	28	15	1.86667	
3	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	0	11083.9	4475.84	2.47638	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	1	28	15	1.86667	
4	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	0	21883	8906	2.45711	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	1	28	15	1.86667	
5	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	0	11965.7	5510.5	2.17144	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	1	28	15	1.86667	
6	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	0	15339.2	7523	2.03897	
7	cab2. [source:refseq;acc:nm_033419]	0	10950	21866	1.99689	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	1	322	215	1.49767	
8	hbs1-like. [source:refseq;acc:nm_006620]	1	322	215	1.49767	
8	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	0	21888	11525	1.89918	
9	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	0	21888	11525	1.89918	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	1	309	212	1.45755	
10	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	0	14178.1	7509.39	1.88805	
10	protein x 0004. [source:refseq;acc:nm_016301]	1	309	212	1.45755	
11	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	0	6248	11627	1.86092	
11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	1	232	337	1.45259	
12	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [source:swissprot;acc:q05932]	0	5208.84	9429.18	1.81023	
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	1	232	337	1.45259	
13	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	0	9264.5	5210.5	1.77804	
13	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	1	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]	1	75.3531	56.6768	1.32952	
14	dystrophin. [source:swissprot;acc:p11532]	0	18054.8	10232.5	1.76446	
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	1	75.3948	56.7244	1.32914	
15	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	0	11267	19403	1.72211	
16	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	0	20670.6	12170.7	1.69839	
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	1	75.3954	56.7252	1.32913	
17	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	1	75.447	56.7841	1.32866	
17	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402]	0	6812	11543	1.69451	
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	1	245.247	185.678	1.32082	
18	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	0	13216	22286	1.68629	
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	1	245.247	185.678	1.32082	
19	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	0	13216	22286	1.68629	
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	1	245.247	185.678	1.32082	
20	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	0	13216	22286	1.68629	
21	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	0	10621.4	6313.38	1.68236	
21	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	1	245.247	185.678	1.32082	
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	1	245.247	185.678	1.32082	
22	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	0	12479	20989	1.68195	
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	1	44	58	1.31818	
23	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [source:refseq;acc:nm_004712]	0	9285.44	15520.4	1.67148	
24	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	0	8257	13730.5	1.66289	
24	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	1	44	58	1.31818	
25	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	0	8257	13730.5	1.66289	
25	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	1	44	58	1.31818	

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/