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

Results: HTML CSV LaTeX

Showing element 418 to 467 of 3228 in total

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

Rank	network_comparison	description	red	green
418	1.15603	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	5493.1	6350.19
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	1.15589	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	10235.2	11830.8
421	1.15582	vav-2 protein. [swissprot;acc:p52735]	6660.02	7697.78
422	1.15425	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	5206.9	6010.04
423	1.15423	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	5207.03	6010.1
424	1.15413	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	5207.78	6010.45
425	1.15354	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	3729.02	4301.58
426	1.15325	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	5942.49	6853.15
427	1.15297	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	11736.6	13531.9
428	1.15237	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	3721.19	4288.17
429	1.15195	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	6272.91	7226.06
430	1.15123	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	3804.09	4379.37
431	1.15102	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	3849.94	4431.36
432	1.15093	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	5244.71	6036.27
433	1.15091	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713]	5244.88	6036.38
434	1.15077	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	5246.38	6037.37
435	1.1507	proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903]	5233.86	6022.6
436	1.15042	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	6230.94	7168.2
437		suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	3779.92	4348.48
438	1.15039	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
439		programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]
440	1.15038	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	6251.91	7192.08
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	1.15011	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	3758.67	4322.87
445	1.14978	ad24 protein. [refseq;acc:nm_022451]	3753.71	4315.95
446	1.14958	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	3766.03	4329.37
447	1.14922	pescadillo homolog 1. [swissprot;acc:o00541]	3751.14	4310.89
448	1.14884	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	6259.3	7190.91
449	1.14837	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	3761.59	4319.69
450	1.14753	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	4889.21	5610.52
451	1.14745	n-myc proto-oncogene protein. [swissprot;acc:p04198]	4889.71	5610.69
452	1.14738	zinc finger-like protein 9. [refseq;acc:nm_033414]	3760.8	4315.06
453		membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
454		guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
455	1.14731	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	4890.51	5610.95
456		ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545]
457		nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217]
458		elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]	4890.55	5610.96
459	1.14704	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	4892.16	5611.48
460	1.14693	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	3790.11	4346.98
461	1.14683	grb2-related adaptor protein. [swissprot;acc:q13588]	5986.65	6865.68
462	1.14674	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	11383.2	9926.61
463	1.1463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	3720.18	4264.46
464	1.1461	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	4858.96	5568.85
465	1.14605	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	3847.31	4409.22
466		transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
467	1.14583	metastasis-associated protein mta1. [swissprot;acc:q13330]	4864.25	5573.62

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.