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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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

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/