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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 980 to 1029 of 8289 in total

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

Rank	description	Hugo	Interaction Map	red	green	network_comparison
490	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]	TMOD1	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]	GTPBP4	High confidence	251.83	234.951	1.07184
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	SNX9	Low confidence	209.136	202.478	1.03288
492	neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]	TMOD2
	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]	PAK2	High confidence	220.171	235.979	1.0718
493	activated p21cdc42hs kinase. [refseq;acc:nm_005781]	TNK2	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]	COG5	High confidence	220.172	235.98	1.0718
494	elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534]	EEF1B2	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]	PAK1	High confidence	220.172	235.98	1.0718
495	lim domains containing 1. [refseq;acc:nm_014240]	LIMD1	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]	PAK3	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]	no value	Low confidence	203.117	196.671	1.03278
	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	PPAN-P2RY11	High confidence	250.938	234.134	1.07177
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	EBNA1BP2		251.344	234.514
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	SF4	Low confidence	203.117	196.671	1.03278
498	kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845]	KIFAP3
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	ARHGEF6	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]	POLI	Low confidence	203.167	196.732	1.03271
	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	TPI1	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]	ING2		224.662	240.673	1.07127
	rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8]	RCL1	Low confidence	203.85	197.403	1.03266
501	calcyphosine. [swissprot;acc:q13938]	CAPS		204.363	197.899
	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	CYC1	High confidence	238.704	255.68	1.07112
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]	ARHGAP26
	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]	SART1	Low confidence	200.271	193.957	1.03255
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]	RGN	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]	USP22	Low confidence	207.407	200.869	1.03255
504	oligophrenin 1. [swissprot;acc:o60890]	OPHN1	High confidence	238.704	255.68	1.07112
	zinc finger protein 183. [swissprot;acc:o15541]	RNF113A	Low confidence	205.192	198.726	1.03254
505	ad24 protein. [refseq;acc:nm_022451]	NOC3L	High confidence	251.334	234.672	1.071
	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	PCNA	Low confidence	207.84	201.297	1.0325
506	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	ING1	High confidence	224.535	240.476	1.071
	putative fork head domain transcription factor afx1 (forkhead box protein o4). [swissprot;acc:p98177]	FOXO4	Low confidence	205.157	198.715	1.03242
507	hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	no value
	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	WDR12	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]	APP	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]	CPA3	High confidence	177.698	190.24	1.07058
509	carboxypeptidase b precursor. [refseq;acc:nm_020361]	CPA6			190.239	1.07057
	tweety homolog 2. [refseq;acc:nm_032646]	TTYH2	Low confidence	205.157	198.715	1.03242
510	hemoglobin zeta chain (hbaz). [swissprot;acc:p02008]	HBZ
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	CPB2	High confidence	177.699	190.24	1.07057
511	alpha 2 globin. [refseq;acc:nm_000517]	no value	Low confidence	205.157	198.715	1.03242
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	NOL1	High confidence	250.053	233.725	1.06986
512	amyloid-like protein 1 precursor (aplp) (aplp-1) [contains: c30]. [swissprot;acc:p51693]	APLP1	Low confidence	205.157	198.715	1.03242
	block of proliferation 1. [swissprot;acc:q14137]	BOP1	High confidence	250.794	234.433	1.06979
513	myoglobin. [swissprot;acc:p02144]	no value	Low confidence	205.157	198.715	1.03242
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	DVL1	High confidence	218.596	204.344	1.06975
514	hemoglobin theta-1 chain. [swissprot;acc:p09105]	HBQ1	Low confidence	205.157	198.715	1.03242
	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	DVL2	High confidence	218.613	204.382	1.06963
515	pescadillo homolog 1. [swissprot;acc:o00541]	PES1		251.297	234.941	1.06962

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.