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 375 to 424 of 3228 in total

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

Rank	description	red	green	network_comparison
375	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	4700.42	5492.63	1.16854
376	44050 protein. [refseq;acc:nm_178832]	17385.9	14889.2	1.16769
377	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]
378	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	12471.7	14561.7	1.16758
379	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	6704.44	7811.45	1.16512
380	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	12998.5	15138.2	1.16461
381	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	5246.01	6109.31	1.16456
382	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	4533.74	5279.4	1.16447
383	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
384	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
385	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]
386	60s ribosomal protein l8. [swissprot;acc:p25120]
387	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]
389	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]
390	rw1 protein (fragment). [swissprot;acc:q92545]
391	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	3658.76	3144.39	1.16358
392	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	3641.89	4236.95	1.16339
393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	4490.28	5222.25	1.16301
394	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]
395	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	4532.73	5269.33	1.16251
396	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	6563.65	7627.29	1.16205
397	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	5367.04	6233.12	1.16137
398	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	5084.26	5904.1	1.16125
399	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	5201.41	4479.76	1.16109
400	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
401	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]
402	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]
403	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
404	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]
405	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]
406	thymic stromal co-transporter. [refseq;acc:nm_033051]
407	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	6603.41	7664.65	1.16071
408	dok-like protein. [refseq;acc:nm_024872]	6102.59	7081.46	1.1604
409	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]
410	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]
411	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]
412	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	3594.31	4169.95	1.16015
413	vav proto-oncogene. [swissprot;acc:p15498]	6644.99	7707.8	1.15994
414	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	6744.05	5815.13	1.15974
415	vav-3 protein. [swissprot;acc:q9ukw4]	6647.43	7706.18	1.15927
416	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	4509.54	5223.95	1.15842
417	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	4522.71	5233.14	1.15708
418	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	5493.1	6350.19	1.15603
419	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]
420	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	10235.2	11830.8	1.15589
421	vav-2 protein. [swissprot;acc:p52735]	6660.02	7697.78	1.15582
422	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	5206.9	6010.04	1.15425
423	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	5207.03	6010.1	1.15423
424	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	5207.78	6010.45	1.15413

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.