MK5 Microarray Data

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	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 1313 to 1362 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
1313	60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809]	5457.14	5899.85	1.08112
1314	vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7]	5401.39	5838.63	1.08095
1315	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098]	5685.77	6145.43	1.08084
1316	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	6105.93	6599.41	1.08082
1317	orphan nuclear receptor tr2. [swissprot;acc:p13056]	6105.69	6599.06	1.0808
1318	serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6]	5961.97	6443.07	1.08069
1319	serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956]
1320	glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]
1321	suppressor of var1, 3-like 1. [refseq;acc:nm_003171]	6439.79	6959.21	1.08066
1322	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
1323	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840]
1324	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841]
1325	serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209]	5656.79	6112.02	1.08047
1326	mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620]	6222.8	6723.54
1327	p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671]	5656.8	6111.9	1.08045
1328	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	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	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	5779.83	6244.56	1.08041
1331	transaldolase (ec 2.2.1.2). [swissprot;acc:p37837]	5799.29	6265.2	1.08034
1332	my016 protein. [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. [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. [refseq;acc:nm_005470]	5804.75	6270.15	1.08018
1335	coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618]	10430.3	9656.4	1.08014
1336	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170]	6140.18	6632.24
1337	gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793]	4935.58	5329.93	1.0799
1338	megf6 (fragment). [sptrembl;acc:o75095]	5980.41	6457.51	1.07978
1339	6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [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). [swissprot;acc:p28070]	5979.07	6453.53	1.07935
1341	alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609]	5887.82	6354.58	1.07928
1342	dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [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). [swissprot;acc:q13627]		6354.5	1.07925
1344	elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040]
1345	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	alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707]	5887.89	6354.45	1.07924
1347	presenilins associated rhomboid-like protein. [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). [swissprot;acc:o75936]
1349	potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]
1350	tetratricopeptide repeat protein 4 (my044 protein). [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). [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). [swissprot;acc:p46734]	6104.11	6586.48	1.07902
1353	cyclin c. [swissprot;acc:p24863]	6200.93	6690.57	1.07896
1354	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	6036.22	6512.64	1.07893
1355	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [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). [swissprot;acc:p53805]	5657.71	6103.57	1.07881
1357	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]		6103.54	1.0788
1358	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1]
1359	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]
1360	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	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8]
1362	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

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.