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 912 to 961 of 8289 in total

Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Interaction Map	red	green	network_comparison
456	single-stranded dna-binding protein, mitochondrial precursor (mt-ssb) (mtssb) (pwp1-interacting protein 17). [swissprot;acc:q04837]	Low confidence	8418.91	8843.31	1.05041
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]	High confidence	4890.51	5610.95	1.14731
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	Low confidence	7577.1	7958.42	1.05033
458	dnaj homolog subfamily c member x (beta cysteine string protein) (beta-csp). [swissprot;acc:q9uf47]		8945.87	9395.73	1.05029
	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]	High confidence	4890.55	5610.96	1.14731
459	dnaj homolog subfamily c member 5 (cysteine string protein) (csp). [swissprot;acc:q9h3z4]	Low confidence	8946.01	9395.86	1.05028
	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	High confidence	4892.16	5611.48	1.14704
460	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]		3790.11	4346.98	1.14693
	pr-domain zinc finger protein 1 (beta-interferon gene positive- regulatory domain i binding factor) (blimp-1) (positive regulatory domain i-binding factor 1) (prdi-binding factor-1) (prdi-bf1). [swissprot;acc:o75626]	Low confidence	8866.09	9311.18	1.0502
461	grb2-related adaptor protein. [swissprot;acc:q13588]	High confidence	5986.65	6865.68	1.14683
	pr-domain zinc finger protein 12. [swissprot;acc:q9h4q4]	Low confidence	8864.55	9309.3	1.05017
462	pr-domain zinc finger protein 7. [swissprot;acc:q9nqw5]		8864.53	9309.27
	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]	High confidence	11383.2	9926.61	1.14674
463	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	Low confidence	8844.87	9288.13	1.05011
	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	High confidence	3720.18	4264.46	1.1463
464	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
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Low confidence	7847.59	8240.61	1.05008
465	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]		7580.97	7960.37	1.05005
	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]	High confidence	3847.31	4409.22	1.14605
466	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
	yippee-like protein 2 (digeorge syndrome-related protein fksg4). [swissprot;acc:q96qa6]	Low confidence	8941.56	9388.99	1.05004
467	metastasis-associated protein mta1. [swissprot;acc:q13330]	High confidence	4864.25	5573.62	1.14583
	yippee-like protein 3 (digeorge syndrome-related protein fksg5). [swissprot;acc:q9bsj4]	Low confidence	8941.65	9389.09	1.05004
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]	High confidence	4869.15	5578.02	1.14558
	yippee-like protein 5. [swissprot;acc:q96ns1]	Low confidence	8940.99	9388.34	1.05003
469	lim domains containing 1. [refseq;acc:nm_014240]		7702.99	8088.26	1.05002
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	High confidence	3831.17	4388.74	1.14554
470	block of proliferation 1. [swissprot;acc:q14137]		3796.24	4348.59	1.1455
	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1]	Low confidence	7702.99	8088.26	1.05002
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]	High confidence	9649.61	11053.5	1.14549
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Low confidence	7702.99	8088.26	1.05002
472	kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845]
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	High confidence	9649.61	11053.5	1.14549
473	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Low confidence	8840.55	9282.64	1.05001
	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]	High confidence	9649.61	11053.5	1.14549
474	aquaporin 5. [swissprot;acc:p55064]	Low confidence	8840.55	9282.64	1.05001
	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]	High confidence	9649.61	11053.5	1.14549
475	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Low confidence	8840.53	9282.62	1.05001
	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	High confidence	9649.61	11053.5	1.14549
476	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	Low confidence	8840.39	9282.37	1.05
	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	High confidence	9649.61	11053.5	1.14549
477	nitrogen fixation cluster-like. [refseq;acc:nm_014301]
	prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9]	Low confidence	8444.05	8865.49	1.04991
478	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	High confidence	9649.61	11053.5	1.14549
	uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9]	Low confidence	8444.05	8865.49	1.04991
479	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]		8754.87	9190.49	1.04976
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	High confidence	9649.61	11053.5	1.14549
480	bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8]	Low confidence	8459.92	8880.14	1.04967
	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]	High confidence	9649.61	11053.5	1.14549
481	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	Low confidence	7722.25	8104.32	1.04948

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.