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

Results: HTML CSV LaTeX

Showing element 1208 to 1257 of 3228 in total

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

Rank	description	red	green	network_comparison
1208	meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	5913.73	6423.98	1.08628
1209	bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814]	5420.87	5887.53	1.08609
1210	trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6]	6410.73	6962.22	1.08603
1211	gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
1212	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	4077.89	4428.28	1.08592
1213	branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687]	5890.62	6396.53	1.08588
1214	mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318]	6001.16	6515.9	1.08577
1215	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382]	5892.05	6397.28	1.08575
1216	fibulin-2 precursor. [swissprot;acc:p98095]	8670.59	9412.9	1.08561
1217	cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708]	6021.21	6536.45	1.08557
1218	cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184]	5736	6226.52	1.08552
1219	tcd37 homolog; prune. [refseq;acc:nm_021222]	5735.95	6226.46
1220	cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623]	5735.65	6226.13	1.08551
1221	cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649]	5736.34	6226.88
1222	cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348]	5735.74	6226.23
1223	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	6011.44	6524.55	1.08536
1224	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427]	4331.35	4700.91	1.08532
1225	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481]	5546.5	6019.57	1.08529
1226	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	5997.24	6508.62	1.08527
1227	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	5973.95	6483.32
1228	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	5998.58	6509.65	1.0852
1229	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	5998.69	6509.74	1.08519
1230	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	5678.02	6161.65	1.08518
1231	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2]	5132.68	5569.54	1.08511
1232	nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384]	5869.24	6367.8	1.08494
1233	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679]	6004.54	6514.24	1.08489
1234	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245]	5807.83	6300.47	1.08482
1235	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
1236	p10-binding protein. [refseq;acc:nm_024491]	5594.18	6067.49	1.08461
1237	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8]	5873.56	6370.31	1.08457
1238	sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676]
1239	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	5654.53	6132.76
1240	retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338]	5654.54	6132.69	1.08456
1241	26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200]	6436.19	6980.13	1.08451
1242	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965]	11143.5	10276.3	1.08439
1243	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357]
1244	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	4835.55	5243.23	1.08431
1245	casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
1246	p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44]	5346.11	5796.72	1.08429
1247	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	6278.76	6807.51	1.08421
1248	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706]	6275.86	6803.95	1.08415
1249	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	4413.55	4784.6	1.08407
1250	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	10733.4	9902.6	1.0839
1251	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	8618.32	9340.98	1.08385
1252	zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315]
1253	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275]
1254	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	10725.6	9896.32	1.0838
1255	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172]	5438.66	5893.87	1.0837
1256	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	10719	9891.08
1257	immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318]	5438.66	5893.87

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.