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

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Showing element 425 to 474 of 12912 in total

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

Rank	Hugo	description	red	green	network_comparison
425	NIP7	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	3729.02	4301.58	1.15354
426	PEF1	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	5942.49	6853.15	1.15325
427	TRMU	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	11736.6	13531.9	1.15297
428	GTPBP4	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	3721.19	4288.17	1.15237
429	SORBS3	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	6272.91	7226.06	1.15195
430	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	3804.09	4379.37	1.15123
431	DDX31	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	PMPCB	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	PMPCA	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	UQCRC1	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	PROSC	proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903]	5233.86	6022.6	1.1507
436	SORBS2	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	6230.94	7168.2	1.15042
437	PPAN-P2RY11	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	3779.92	4348.48
438	ARID1A	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	PDCD6	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]
440	CAPNS1	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	6251.91	7192.08	1.15038
441	GCA	grancalcin. [swissprot;acc:p28676]	6251.96	7192.13
442	SRI	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	6251.99	7192.17
443	ARID1B	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	6252.27	7192.51
444	EBNA1BP2	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	3758.67	4322.87	1.15011
445	NOC3L	ad24 protein. [refseq;acc:nm_022451]	3753.71	4315.95	1.14978
446	GNL3	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	3766.03	4329.37	1.14958
447	PES1	pescadillo homolog 1. [swissprot;acc:o00541]	3751.14	4310.89	1.14922
448	SORBS1	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	6259.3	7190.91	1.14884
449	WDR12	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	3761.59	4319.69	1.14837
450	MYCL1	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	4889.21	5610.52	1.14753
451	MYCN	n-myc proto-oncogene protein. [swissprot;acc:p04198]	4889.71	5610.69	1.14745
452	ZNF622	zinc finger-like protein 9. [refseq;acc:nm_033414]	3760.8	4315.06	1.14738
453	SLC45A2	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
454	no value	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
455	GABPA	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	1.14731
456	no value	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	NDUFS8	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	ELOVL1	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]	4890.55	5610.96
459	MYC	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	4892.16	5611.48	1.14704
460	RRP1	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	3790.11	4346.98	1.14693
461	GRAP	grb2-related adaptor protein. [swissprot;acc:q13588]	5986.65	6865.68	1.14683
462	no value	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	1.14674
463	DDX18	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	3720.18	4264.46	1.1463
464	RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	4858.96	5568.85	1.1461
465	E2F1	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	1.14605
466	E2F2	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
467	MTA1	metastasis-associated protein mta1. [swissprot;acc:q13330]	4864.25	5573.62	1.14583
468	RBBP4	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	5578.02	1.14558
469	NOL1	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	3831.17	4388.74	1.14554
470	BOP1	block of proliferation 1. [swissprot;acc:q14137]	3796.24	4348.59	1.1455
471	MAPK11	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	11053.5	1.14549
472	SPHK1	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]
473	DPAGT1	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	DLC1	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]

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
- Hugo is the HGNC identifier if it exists
- 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.