Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1975 to 2024 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Value Type	description	red	green	network_comparison	
494	Squared	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [source:swissprot;acc:p13804]	31583	37925.6	1.20082	
494	Rooted	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [source:refseq;acc:nm_033222]	55.1759	60.2621	1.09218	
495	Measured	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	10804.7	12363.6	1.14428	
495	Ranked	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [source:swissprot;acc:o75914]	220.171	235.979	1.0718	
495	Squared	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	30286.5	36362	1.2006	
495	Rooted	60s ribosomal protein l8. [source:swissprot;acc:p25120]	55.1759	60.2621	1.09218	
496	Measured	nostrin. [source:refseq;acc:nm_052946]	4682.87	4093.05	1.1441	
496	Ranked	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	250.938	234.134	1.07177	
496	Squared	tubby protein homolog. [source:swissprot;acc:p50607]	30286.5	36362	1.2006	
496	Rooted	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [source:swissprot;acc:p51858]	55.1759	60.2621	1.09218	
497	Measured	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	4682.87	4093.05	1.1441	
497	Ranked	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	251.344	234.514	1.07177	
497	Squared	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [source:swissprot;acc:p41743]	30286.5	36362	1.2006	
497	Rooted	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	55.1759	60.2621	1.09218	
498	Measured	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	4682.87	4093.05	1.1441	
498	Ranked	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	220.161	235.95	1.07172	
498	Squared	numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	30286.5	36362	1.2006	
498	Rooted	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	55.1759	60.2621	1.09218	
499	Measured	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	4682.87	4093.05	1.1441	
499	Ranked	triosephosphate isomerase (ec 5.3.1.1) (tim). [source:swissprot;acc:p00938]	231.496	248.048	1.0715	
499	Squared	tbc1 domain family member 5. [source:swissprot;acc:q92609]	30286.5	36362	1.2006	
499	Rooted	rw1 protein (fragment). [source:swissprot;acc:q92545]	55.1759	60.2621	1.09218	
500	Measured	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	4682.87	4093.05	1.1441	
500	Ranked	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	224.662	240.673	1.07127	
500	Squared	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	30286.5	36362	1.2006	
500	Rooted	60s ribosomal protein l7. [source:swissprot;acc:p18124]	52.6483	48.2135	1.09198	
501	Measured	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	4682.87	4093.05	1.1441	
501	Ranked	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	238.704	255.68	1.07112	
501	Squared	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	30286.5	36362	1.2006	
501	Rooted	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	50.4253	46.1792	1.09195	
502	Measured	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	6913.6	7907.05	1.1437	
502	Ranked	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	238.704	255.68	1.07112	
502	Squared	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	30286.5	36362	1.2006	
502	Rooted	60s ribosomal protein l30. [source:swissprot;acc:p04645]	50.4616	46.2257	1.09164	
503	Measured	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [source:swissprot;acc:q13625]	15182.5	13277.9	1.14344	
503	Ranked	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	238.704	255.68	1.07112	
503	Squared	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	30286.5	36362	1.2006	
503	Rooted	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	177.987	194.29	1.0916	
504	Measured	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [source:swissprot;acc:p30084]	10067.9	11511	1.14334	
504	Ranked	oligophrenin 1. [source:swissprot;acc:o60890]	238.704	255.68	1.07112	
504	Squared	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	30286.5	36362	1.2006	
504	Rooted	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	144.606	157.824	1.09141	
505	Measured	signal transduction protein cbl-b (sh3-binding protein cbl-b). [source:swissprot;acc:q13191]	6856.71	7838.3	1.14316	
505	Ranked	ad24 protein. [source:refseq;acc:nm_022451]	251.334	234.672	1.071	
505	Squared	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	30286.5	36362	1.2006	
505	Rooted	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	144.606	157.824	1.09141	
506	Measured	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	3893.85	4450.98	1.14308	
506	Ranked	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	224.535	240.476	1.071	
506	Squared	vav-2 protein. [source:swissprot;acc:p52735]	31377.3	37670.1	1.20055	
506	Rooted	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	144.606	157.824	1.09141	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/