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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Value Type Rank Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1327 to 1376 of 12912 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
1327 OCA2 p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] 5656.8 6111.9 1.08045
1328 PPP3CB serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] 5656.81 6111.84 1.08044
1329 PPP3CC serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] 5656.82 6111.8 1.08043
1330 no value isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 5779.83 6244.56 1.08041
1331 TALDO1 transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] 5799.29 6265.2 1.08034
1332 BOLA2B my016 protein. [sptrembl;acc:q9h3k6] 4775.25 5158.86 1.08033
1333 ABI2 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. [refseq;acc:nm_005759] 5803.95 6269.44 1.0802
1334 ABI1 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] 5804.75 6270.15 1.08018
1335 COPB1 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] 10430.3 9656.4 1.08014
1336 GSPT1 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 6140.18 6632.24
1337 GCH1 gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] 4935.58 5329.93 1.0799
1338 MEGF6 megf6 (fragment). [sptrembl;acc:o75095] 5980.41 6457.51 1.07978
1339 PGD 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 5988.06 6464.94 1.07964
1340 PSMB4 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). [swissprot;acc:p28070] 5979.07 6453.53 1.07935
1341 ACTN2 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] 5887.82 6354.58 1.07928
1342 DYRK1B dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] 5887.86 6354.51 1.07926
1343 DYRK1A dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] 6354.5 1.07925
1344 ELP4 elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040]
1345 ACTN1 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] 5887.88 6354.47
1346 ACTN4 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] 5887.89 6354.45 1.07924
1347 PARL presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 6153.36 6640.77 1.07921
1348 BBOX1 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]
1349 ATP11A potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]
1350 no value tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] 6783.78 7320.39 1.0791
1351 MAP2K6 dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] 6105.23 6587.88 1.07906
1352 MAP2K3 dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] 6104.11 6586.48 1.07902
1353 CCNC cyclin c. [swissprot;acc:p24863] 6200.93 6690.57 1.07896
1354 ACTG1 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 6036.22 6512.64 1.07893
1355 OTC ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 5783.9 6240.19 1.07889
1356 RCAN1 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 5657.71 6103.57 1.07881
1357 CSMD1 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 6103.54 1.0788
1358 ZIC4 zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1]
1359 no value dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]
1360 RCAN2 calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] 5657.72 6103.52 1.07879
1361 RCAN3 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8]
1362 SQSTM1 sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] 6322.75 6820.5 1.07872
1363 SCP2 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]
1364 C20orf4 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] 5815.14 6272.66 1.07868
1365 ADD3 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 5799.14 6255.04 1.07862
1366 MEGF11 megf11 protein. [refseq;acc:nm_032445] 5793.55 6248.79 1.07858
1367 MEGF10 megf10 protein. [refseq;acc:nm_032446] 5793.47 6248.71
1368 ADD2 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 5793.29 6248.51
1369 ADD1 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 5786.71 6241.16 1.07853
1370 DYNLT3 t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] 10231.8 9487.34 1.07847
1371 MRE11A double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]
1372 LIN7A lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] 5743.45 6193.45 1.07835
1373 MAPK3 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). [swissprot;acc:p27361] 6079.85 6556.07 1.07833
1374 RPS6KA3 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). [swissprot;acc:p51812] 6079.45 6555.4 1.07829
1375 CAMK2G 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). [swissprot;acc:q13555]
1376 CAMK2D 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). [swissprot;acc:q13557] 6079.46 6555.41

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
- 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/