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 green network_comparison
Results: HTML CSV LaTeX Showing element 1330 to 1379 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1330	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	5779.83	6244.56	1.08041	
1331	transaldolase (ec 2.2.1.2). [source:swissprot;acc:p37837]	5799.29	6265.2	1.08034	
1332	my016 protein. [source:sptrembl;acc:q9h3k6]	4775.25	5158.86	1.08033	
1333	abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [source:refseq;acc:nm_005759]	5803.95	6269.44	1.0802	
1334	spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [source:refseq;acc:nm_005470]	5804.75	6270.15	1.08018	
1335	coatomer beta subunit (beta-coat protein) (beta-cop). [source:swissprot;acc:p53618]	10430.3	9656.4	1.08014	
1336	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [source:swissprot;acc:p15170]	6140.18	6632.24	1.08014	
1337	gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [source:swissprot;acc:p30793]	4935.58	5329.93	1.0799	
1338	megf6 (fragment). [source:sptrembl;acc:o75095]	5980.41	6457.51	1.07978	
1339	6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	5988.06	6464.94	1.07964	
1340	proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [source:swissprot;acc:p28070]	5979.07	6453.53	1.07935	
1341	alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [source:swissprot;acc:p35609]	5887.82	6354.58	1.07928	
1342	dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [source:swissprot;acc:q9y463]	5887.86	6354.51	1.07926	
1343	dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [source:swissprot;acc:q13627]	5887.86	6354.5	1.07925	
1344	elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [source:refseq;acc:nm_019040]	5887.86	6354.5	1.07925	
1345	alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [source:swissprot;acc:p12814]	5887.88	6354.47	1.07925	
1346	alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [source:swissprot;acc:o43707]	5887.89	6354.45	1.07924	
1347	presenilins associated rhomboid-like protein. [source:refseq;acc:nm_018622]	6153.36	6640.77	1.07921	
1348	gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [source:swissprot;acc:o75936]	6153.36	6640.77	1.07921	
1349	potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [source:swissprot;acc:p98196]	6153.36	6640.77	1.07921	
1350	tetratricopeptide repeat protein 4 (my044 protein). [source:swissprot;acc:o95801]	6783.78	7320.39	1.0791	
1351	dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [source:swissprot;acc:p52564]	6105.23	6587.88	1.07906	
1352	dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [source:swissprot;acc:p46734]	6104.11	6586.48	1.07902	
1353	cyclin c. [source:swissprot;acc:p24863]	6200.93	6690.57	1.07896	
1354	actin, cytoplasmic 2 (gamma-actin). [source:swissprot;acc:p02571]	6036.22	6512.64	1.07893	
1355	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [source:swissprot;acc:p00480]	5783.9	6240.19	1.07889	
1356	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [source:swissprot;acc:p53805]	5657.71	6103.57	1.07881	
1357	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	5657.71	6103.54	1.0788	
1358	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [source:swissprot;acc:q8n9l1]	5657.71	6103.54	1.0788	
1359	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	5657.71	6103.54	1.0788	
1360	calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [source:swissprot;acc:q14206]	5657.72	6103.52	1.07879	
1361	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [source:swissprot;acc:q9uka8]	5657.72	6103.52	1.07879	
1362	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [source:refseq;acc:nm_003900]	6322.75	6820.5	1.07872	
1363	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [source:swissprot;acc:p22307]	6322.75	6820.5	1.07872	
1364	protein c20orf4 (protein cgi-23) (pro0225). [source:swissprot;acc:q9y312]	5815.14	6272.66	1.07868	
1365	gamma adducin (adducin-like protein 70). [source:swissprot;acc:q9uey8]	5799.14	6255.04	1.07862	
1366	megf11 protein. [source:refseq;acc:nm_032445]	5793.55	6248.79	1.07858	
1367	megf10 protein. [source:refseq;acc:nm_032446]	5793.47	6248.71	1.07858	
1368	beta adducin (erythrocyte adducin beta subunit). [source:swissprot;acc:p35612]	5793.29	6248.51	1.07858	
1369	alpha adducin (erythrocyte adducin alpha subunit). [source:swissprot;acc:p35611]	5786.71	6241.16	1.07853	
1370	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	10231.8	9487.34	1.07847	
1371	double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	10231.8	9487.34	1.07847	
1372	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [source:refseq;acc:nm_004664]	5743.45	6193.45	1.07835	
1373	mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [source:swissprot;acc:p27361]	6079.85	6556.07	1.07833	
1374	ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [source:swissprot;acc:p51812]	6079.45	6555.4	1.07829	
1375	calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [source:swissprot;acc:q13555]	6079.45	6555.4	1.07829	
1376	calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [source:swissprot;acc:q13557]	6079.46	6555.41	1.07829	
1377	mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [source:swissprot;acc:o95382]	6079.46	6555.4	1.07829	
1378	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	6079.45	6555.4	1.07829	
1379	ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [source:swissprot;acc:q15418]	6079.46	6555.41	1.07829	

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/