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 975 to 1024 of 8289 in total

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

Rank	description	Interaction Map	red	green	network_comparison
488	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]	Low confidence	209.136	202.478	1.03288
	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	High confidence	225.026	209.798	1.07258
489	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688]		231.276	215.627	1.07257
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Low confidence	209.136	202.478	1.03288
490	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]	High confidence	220.183	236.015	1.0719
	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]	Low confidence	209.136	202.478	1.03288
491	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	High confidence	251.83	234.951	1.07184
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	Low confidence	209.136	202.478	1.03288
492	neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177]	High confidence	220.171	235.979	1.0718
493	activated p21cdc42hs kinase. [refseq;acc:nm_005781]	Low confidence	209.136	202.478	1.03288
	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83]	High confidence	220.172	235.98	1.0718
494	elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534]	Low confidence	206.154	199.596	1.03286
	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153]	High confidence	220.172	235.98	1.0718
495	lim domains containing 1. [refseq;acc:nm_014240]	Low confidence	203.117	196.671	1.03278
	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914]	High confidence	220.171	235.979	1.0718
496	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1]	Low confidence	203.117	196.671	1.03278
	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	High confidence	250.938	234.134	1.07177
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]		251.344	234.514
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Low confidence	203.117	196.671	1.03278
498	kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845]
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	High confidence	220.161	235.95	1.07172
499	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Low confidence	203.167	196.732	1.03271
	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	High confidence	231.496	248.048	1.0715
500	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]		224.662	240.673	1.07127
	rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8]	Low confidence	203.85	197.403	1.03266
501	calcyphosine. [swissprot;acc:q13938]		204.363	197.899
	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	High confidence	238.704	255.68	1.07112
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	Low confidence	200.271	193.957	1.03255
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]	High confidence	238.704	255.68	1.07112
	ubiquitin carboxyl-terminal hydrolase 22 (ec 3.1.2.15) (ubiquitin thiolesterase 22) (ubiquitin-specific processing protease 22) (deubiquitinating enzyme 22) (fragment). [swissprot;acc:q9upt9]	Low confidence	207.407	200.869	1.03255
504	oligophrenin 1. [swissprot;acc:o60890]	High confidence	238.704	255.68	1.07112
	zinc finger protein 183. [swissprot;acc:o15541]	Low confidence	205.192	198.726	1.03254
505	ad24 protein. [refseq;acc:nm_022451]	High confidence	251.334	234.672	1.071
	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	Low confidence	207.84	201.297	1.0325
506	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	High confidence	224.535	240.476	1.071
	putative fork head domain transcription factor afx1 (forkhead box protein o4). [swissprot;acc:p98177]	Low confidence	205.157	198.715	1.03242
507	hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]
	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	High confidence	251.299	234.729	1.07059
508	amyloid beta a4 protein precursor (app) (abpp) (alzheimer's disease amyloid protein) (cerebral vascular amyloid peptide) (cvap) (protease nexin-ii) (pn-ii) (appi) (prea4) [contains: soluble app-alpha (s-app- alpha); soluble app-beta (s-app-beta); c99; beta-amyloid protein 42 (beta-app42); beta-amyloid protein 40 (beta-app40); c83; p3(42); p3(40); gamma-ctf(59) (gamma-secretase c-terminal fragment 59) (amyloid intracellular domain 59) (aid(59)); gamma-ctf(57) (gamma- secretase c-terminal fragment 57) (amyloid intracellular domain 57) (aid(57)); gamma-ctf(50) (gamma-secretase c-terminal fragment 50) (amyloid intracellular domain 50) (aid(50)); c31]. [swissprot;acc:p05067]	Low confidence	205.157	198.715	1.03242
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	High confidence	177.698	190.24	1.07058
509	carboxypeptidase b precursor. [refseq;acc:nm_020361]			190.239	1.07057
	tweety homolog 2. [refseq;acc:nm_032646]	Low confidence	205.157	198.715	1.03242
510	hemoglobin zeta chain (hbaz). [swissprot;acc:p02008]
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	High confidence	177.699	190.24	1.07057
511	alpha 2 globin. [refseq;acc:nm_000517]	Low confidence	205.157	198.715	1.03242
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	High confidence	250.053	233.725	1.06986
512	amyloid-like protein 1 precursor (aplp) (aplp-1) [contains: c30]. [swissprot;acc:p51693]	Low confidence	205.157	198.715	1.03242
	block of proliferation 1. [swissprot;acc:q14137]	High confidence	250.794	234.433	1.06979

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.