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.

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 401 to 450 of 3228 in total

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

Rank	description	red	green	network_comparison
401	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	5201.41	4479.76	1.16109
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
425	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	3729.02	4301.58	1.15354
426	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	5942.49	6853.15	1.15325
427	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	11736.6	13531.9	1.15297
428	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	3721.19	4288.17	1.15237
429	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	6272.91	7226.06	1.15195
430	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	3804.09	4379.37	1.15123
431	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	3849.94	4431.36	1.15102
432	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	5244.71	6036.27	1.15093
433	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713]	5244.88	6036.38	1.15091
434	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	5246.38	6037.37	1.15077
435	proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903]	5233.86	6022.6	1.1507
436	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	6230.94	7168.2	1.15042
437	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	3779.92	4348.48
438	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	6252.58	7192.88	1.15039
439	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]
440	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	6251.91	7192.08	1.15038
441	grancalcin. [swissprot;acc:p28676]	6251.96	7192.13
442	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	6251.99	7192.17
443	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	6252.27	7192.51
444	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	3758.67	4322.87	1.15011
445	ad24 protein. [refseq;acc:nm_022451]	3753.71	4315.95	1.14978
446	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	3766.03	4329.37	1.14958
447	pescadillo homolog 1. [swissprot;acc:o00541]	3751.14	4310.89	1.14922
448	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	6259.3	7190.91	1.14884
449	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	3761.59	4319.69	1.14837
450	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	4889.21	5610.52	1.14753

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.