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

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	Filtered	description	red	network_comparison	green	
1	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	4294	3.70633	15915	
1	1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	10	2.4	24	
2	0	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	5865	2.55362	14977	
2	1	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	1.86667	28	
3	0	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	4475.84	2.47638	11083.9	
3	1	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	15	1.86667	28	
4	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	8906	2.45711	21883	
4	1	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	15	1.86667	28	
5	0	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	5510.5	2.17144	11965.7	
5	1	cytohesin 4. [source:swissprot;acc:q9uia0]	15	1.86667	28	
6	0	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	7523	2.03897	15339.2	
6	1	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	15	1.86667	28	
7	0	cab2. [source:refseq;acc:nm_033419]	21866	1.99689	10950	
7	1	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	215	1.49767	322	
8	0	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	11525	1.89918	21888	
8	1	hbs1-like. [source:refseq;acc:nm_006620]	215	1.49767	322	
9	0	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	11525	1.89918	21888	
9	1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	212	1.45755	309	
10	0	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	7509.39	1.88805	14178.1	
10	1	protein x 0004. [source:refseq;acc:nm_016301]	212	1.45755	309	
11	0	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	11627	1.86092	6248	
11	1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	337	1.45259	232	
12	0	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [source:swissprot;acc:q05932]	9429.18	1.81023	5208.84	
12	1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	337	1.45259	232	
13	0	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	5210.5	1.77804	9264.5	
13	1	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	288.754	1.3585	212.554	
14	0	dystrophin. [source:swissprot;acc:p11532]	10232.5	1.76446	18054.8	
14	1	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	56.6768	1.32952	75.3531	
15	0	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]	19403	1.72211	11267	
15	1	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	56.7244	1.32914	75.3948	
16	0	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	12170.7	1.69839	20670.6	
16	1	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	56.7252	1.32913	75.3954	
17	0	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]	11543	1.69451	6812	
17	1	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	56.7841	1.32866	75.447	
18	0	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	22286	1.68629	13216	
18	1	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	185.678	1.32082	245.247	
19	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	22286	1.68629	13216	
19	1	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	185.678	1.32082	245.247	
20	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	22286	1.68629	13216	
20	1	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	185.678	1.32082	245.247	
21	0	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	6313.38	1.68236	10621.4	
21	1	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	185.678	1.32082	245.247	
22	0	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	20989	1.68195	12479	
22	1	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	185.678	1.32082	245.247	
23	0	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [source:refseq;acc:nm_004712]	15520.4	1.67148	9285.44	
23	1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	58	1.31818	44	
24	0	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	13730.5	1.66289	8257	
24	1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	58	1.31818	44	
25	0	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	13730.5	1.66289	8257	
25	1	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	58	1.31818	44	

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/