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 Value Type description Network Comparison Type Interaction Map red green Filtered 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	red	green	Filtered	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Divided	4294	15915	0	3.70633
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Subtracted	215	322	1	107
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted	8906	21883	0	12977
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	10	24	1	2.4
2	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted	4294	15915	0	11621
	hbs1-like. [refseq;acc:nm_006620]	Subtracted	215	322	1	107
	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). [swissprot;acc:o60476]	Divided	15	28	1	1.86667
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	5865	14977	0	2.55362
3	cab2. [refseq;acc:nm_033419]	Subtracted	21866	10950	0	10916
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Divided	15	28	1	1.86667
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Divided	4475.84	11083.9	0	2.47638
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted	337	232	1	105
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Divided	15	28	1	1.86667
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	8906	21883	0	2.45711
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Subtracted	11525	21888	0	10363
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Subtracted	337	232	1	105
5	cytohesin 4. [swissprot;acc:q9uia0]	Divided	15	28	1	1.86667
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Subtracted	11525	21888	0	10363
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Divided	5510.5	11965.7	0	2.17144
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Subtracted	212	309	1	97
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Divided	15	28	1	1.86667
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Subtracted	5865	14977	0	9112
	protein x 0004. [refseq;acc:nm_016301]	Subtracted	212	309	1	97
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Divided	7523	15339.2	0	2.03897
7	cab2. [refseq;acc:nm_033419]		21866	10950	0	1.99689
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		215	322	1	1.49767
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Subtracted	22286	13216	0	9070
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted	288.754	212.554	1	76.2
8	hbs1-like. [refseq;acc:nm_006620]	Divided	215	322	1	1.49767
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	22286	13216	0	9070
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Subtracted	288	362	1	74
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	11525	21888	0	1.89918
9	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Subtracted	22286	13216	0	9070
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Subtracted	288	362	1	74
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	11525	21888	0	1.89918
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		212	309	1	1.45755
10	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]		7509.39	14178.1	0	1.88805
	protein x 0004. [refseq;acc:nm_016301]		212	309	1	1.45755
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Subtracted	20989	12479	0	8510
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]		288	362	1	74
11	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]		12170.7	20670.6	0	8499.9
	db83 protein. [swissprot;acc:p57088]		288	362	1	74
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Divided	11627	6248	0	1.86092
	rad50-interacting protein 1. [refseq;acc:nm_021930]		337	232	1	1.45259
12	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]		9429.18	5208.84	0	1.81023
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Subtracted	266.856	336.233	1	69.377
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	337	232	1	1.45259
	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). [swissprot;acc:o14521]	Subtracted	19403	11267	0	8136
13	dystrophin. [swissprot;acc:p11532]		10232.5	18054.8	0	7822.3
13	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]		266.856	336.233	1	69.377

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/