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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 7460 in total

Value Type	Ranked
Interaction Map	High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison	
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Divided	0	4294	15915	3.70633	
1	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Subtracted	1	215	322	107	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Subtracted	0	8906	21883	12977	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Divided	1	10	24	2.4	
2	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Subtracted	0	4294	15915	11621	
2	hbs1-like. [source:refseq;acc:nm_006620]	Subtracted	1	215	322	107	
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]	Divided	1	15	28	1.86667	
2	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Divided	0	5865	14977	2.55362	
3	cab2. [source:refseq;acc:nm_033419]	Subtracted	0	21866	10950	10916	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Divided	1	15	28	1.86667	
3	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	Divided	0	4475.84	11083.9	2.47638	
3	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	1	337	232	105	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Divided	1	15	28	1.86667	
4	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Divided	0	8906	21883	2.45711	
4	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Subtracted	0	11525	21888	10363	
4	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	1	337	232	105	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Divided	1	15	28	1.86667	
5	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Subtracted	0	11525	21888	10363	
5	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	Divided	0	5510.5	11965.7	2.17144	
5	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Subtracted	1	212	309	97	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Divided	1	15	28	1.86667	
6	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Subtracted	0	5865	14977	9112	
6	protein x 0004. [source:refseq;acc:nm_016301]	Subtracted	1	212	309	97	
6	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	Divided	0	7523	15339.2	2.03897	
7	cab2. [source:refseq;acc:nm_033419]	Divided	0	21866	10950	1.99689	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	1	215	322	1.49767	
7	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Subtracted	0	22286	13216	9070	
7	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Subtracted	1	288.754	212.554	76.2	
8	hbs1-like. [source:refseq;acc:nm_006620]	Divided	1	215	322	1.49767	
8	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Subtracted	0	22286	13216	9070	
8	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Subtracted	1	288	362	74	
8	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Divided	0	11525	21888	1.89918	
9	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Subtracted	0	22286	13216	9070	
9	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Subtracted	1	288	362	74	
9	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Divided	0	11525	21888	1.89918	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Divided	1	212	309	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]	Divided	0	7509.39	14178.1	1.88805	
10	protein x 0004. [source:refseq;acc:nm_016301]	Divided	1	212	309	1.45755	
10	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Subtracted	0	20989	12479	8510	
10	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Subtracted	1	288	362	74	
11	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	Subtracted	0	12170.7	20670.6	8499.9	
11	db83 protein. [source:swissprot;acc:p57088]	Subtracted	1	288	362	74	
11	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	Divided	0	11627	6248	1.86092	
11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	1	337	232	1.45259	
12	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [source:swissprot;acc:q05932]	Divided	0	9429.18	5208.84	1.81023	
12	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Subtracted	1	266.856	336.233	69.377	
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	1	337	232	1.45259	
12	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]	Subtracted	0	19403	11267	8136	
13	dystrophin. [source:swissprot;acc:p11532]	Subtracted	0	10232.5	18054.8	7822.3	
13	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	Subtracted	1	266.856	336.233	69.377	

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/