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	network_comparison	green

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Showing element 430 to 479 of 3228 in total

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

Rank	description	red	network_comparison	green
430	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	3804.09	1.15123	4379.37
431	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	3849.94	1.15102	4431.36
432	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	5244.71	1.15093	6036.27
433	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713]	5244.88	1.15091	6036.38
434	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	5246.38	1.15077	6037.37
435	proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903]	5233.86	1.1507	6022.6
436	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	6230.94	1.15042	7168.2
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	1.15039	7192.88
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	1.15038	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	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	3758.67	1.15011	4322.87
445	ad24 protein. [refseq;acc:nm_022451]	3753.71	1.14978	4315.95
446	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	3766.03	1.14958	4329.37
447	pescadillo homolog 1. [swissprot;acc:o00541]	3751.14	1.14922	4310.89
448	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	6259.3	1.14884	7190.91
449	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	3761.59	1.14837	4319.69
450	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	4889.21	1.14753	5610.52
451	n-myc proto-oncogene protein. [swissprot;acc:p04198]	4889.71	1.14745	5610.69
452	zinc finger-like protein 9. [refseq;acc:nm_033414]	3760.8	1.14738	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	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	4890.51	1.14731	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	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	4892.16	1.14704	5611.48
460	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	3790.11	1.14693	4346.98
461	grb2-related adaptor protein. [swissprot;acc:q13588]	5986.65	1.14683	6865.68
462	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	1.14674	9926.61
463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	3720.18	1.1463	4264.46
464	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	4858.96	1.1461	5568.85
465	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	1.14605	4409.22
466	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
467	metastasis-associated protein mta1. [swissprot;acc:q13330]	4864.25	1.14583	5573.62
468	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	4869.15	1.14558	5578.02
469	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	3831.17	1.14554	4388.74
470	block of proliferation 1. [swissprot;acc:q14137]	3796.24	1.1455	4348.59
471	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	9649.61	1.14549	11053.5
472	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]
473	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]
474	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]
475	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]
476	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]
477	nitrogen fixation cluster-like. [refseq;acc:nm_014301]
478	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]
479	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]

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.