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.

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

Results: HTML CSV LaTeX

Showing element 2308 to 2357 of 3228 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
2308	PRKX	protein kinase pkx1 (ec 2.7.1.-). [source:swissprot;acc:p51817]	215.543	214.459	1.00505	
2309	PRKACG	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [source:swissprot;acc:p22612]	215.542	214.459	1.00505	
2310	UBC	ubiquitin. [source:swissprot;acc:p02248]	216.617	215.529	1.00505	
2311	PRKACB	camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [source:swissprot;acc:p22694]	215.542	214.459	1.00505	
2312	PRKACA	camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [source:swissprot;acc:p17612]	215.542	214.459	1.00505	
2313	PRKAR2B	camp-dependent protein kinase type ii-beta regulatory chain. [source:swissprot;acc:p31323]	215.529	214.449	1.00504	
2314	UBE2D2	ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [source:swissprot;acc:p51669]	194.743	195.708	1.00496	
2315	ACACB	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:o00763]	194.825	195.787	1.00494	
2316		26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	217.241	218.311	1.00493	
2317	PPP6C	serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [source:swissprot;acc:o00743]	194.834	195.794	1.00493	
2318	SAPS3	sporulation-induced transcript 4-associated protein. [source:refseq;acc:nm_018312]	194.834	195.794	1.00493	
2319	ACACA	acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:q13085]	194.842	195.8	1.00492	
2320	RAD54L	rad54-like protein; rad54 homolog. [source:refseq;acc:nm_003579]	219.292	218.218	1.00492	
2321		tetratricopeptide repeat protein 4 (my044 protein). [source:swissprot;acc:o95801]	203.909	202.925	1.00485	
2322	PDSS1	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [source:refseq;acc:nm_014317]	236.023	234.905	1.00476	
2323	NARS	asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [source:swissprot;acc:o43776]	192.773	193.691	1.00476	
2324	PSMB1	proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [source:swissprot;acc:p20618]	212.129	211.129	1.00474	
2325	MTFMT	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [source:swissprot;acc:q96dp5]	221.728	220.685	1.00473	
2326	MAP2K4	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [source:swissprot;acc:p45985]	220.076	219.05	1.00468	
2327	PSMC4	26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [source:swissprot;acc:p43686]	217.413	218.426	1.00466	
2328	REXO4	xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [source:refseq;acc:nm_020385]	209.326	208.357	1.00465	
2329	PSMD13	26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [source:swissprot;acc:q9unm6]	217.112	218.116	1.00462	
2330	FARSB	phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [source:swissprot;acc:q9nsd9]	214.213	213.235	1.00459	
2331	MIZF	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [source:refseq;acc:nm_015517]	229.258	230.294	1.00452	
2332	TMOD4	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [source:swissprot;acc:q9nzq9]	229.258	230.294	1.00452	
2333	TMOD3	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [source:swissprot;acc:q9nyl9]	229.258	230.294	1.00452	
2334	TMOD1	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [source:swissprot;acc:p28289]	229.258	230.294	1.00452	
2335	SNX9	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [source:swissprot;acc:q9y5x1]	229.258	230.294	1.00452	
2336	TMOD2	neuronal tropomodulin (n-tmod) (tropomodulin 2). [source:swissprot;acc:q9nzr1]	229.258	230.294	1.00452	
2337	DLX2	homeobox protein dlx-2. [source:swissprot;acc:q07687]	229.258	230.294	1.00452	
2338	DLX5	homeobox protein dlx-5. [source:swissprot;acc:p56178]	229.258	230.294	1.00452	
2339	MPPED2	fetal brain protein 239 (239fb). [source:swissprot;acc:q15777]	229.258	230.294	1.00452	
2340	DLX3	homeobox protein dlx-3. [source:swissprot;acc:o60479]	229.258	230.294	1.00452	
2341	TNK2	activated p21cdc42hs kinase. [source:refseq;acc:nm_005781]	229.258	230.294	1.00452	
2342	MAP3K7IP2	mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [source:refseq;acc:nm_015093]	229.258	230.294	1.00452	
2343		glycine cleavage system h protein, mitochondrial precursor. [source:swissprot;acc:p23434]	212.222	211.27	1.00451	
2344	DAGLB	kccr13l. [source:refseq;acc:nm_139179]	219.878	218.893	1.0045	
2345	RAD51	dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [source:swissprot;acc:q06609]	219.878	218.893	1.0045	
2346	NEK1	serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [source:swissprot;acc:q96py6]	217.057	218.03	1.00448	
2347	NEK3	serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [source:swissprot;acc:p51956]	217.057	218.03	1.00448	
2348	GAPDH	glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [source:swissprot;acc:p04406]	217.057	218.03	1.00448	
2349	FBLN1	fibulin-1 precursor. [source:swissprot;acc:p23142]	192.348	191.503	1.00441	
2350	CNDP2	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [source:swissprot;acc:q96kp4]	209.811	210.733	1.00439	
2351	SYT12	synaptotagmin xii (sytxii). [source:swissprot;acc:q8iv01]	214.223	213.289	1.00438	
2352	ATP7A	copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [source:swissprot;acc:q04656]	215.088	214.155	1.00436	
2353	ETFB	electron transfer flavoprotein beta-subunit (beta-etf). [source:swissprot;acc:p38117]	182.232	183.027	1.00436	
2354	ATP7B	copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [source:swissprot;acc:p35670]	215.078	214.148	1.00434	
2355	PSMD7	26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [source:swissprot;acc:p51665]	217.232	218.162	1.00428	
2356		importin 4. [source:refseq;acc:nm_024658]	220.921	221.863	1.00426	
2357	UBE2G2	ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [source:swissprot;acc:p56554]	198.181	197.346	1.00423	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/