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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2530 to 2579 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2530	proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [source:swissprot;acc:p28062]	212.464	211.99	1.00224	
2531	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [source:refseq;acc:nm_014481]	216.264	215.787	1.00221	
2532	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	190.405	190.812	1.00214	
2533	paraspeckle protein 1. [source:refseq;acc:nm_018282]	190.417	190.824	1.00214	
2534	glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [source:swissprot;acc:p43304]	208	207.555	1.00214	
2535	chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [source:swissprot;acc:p23197]	188.228	188.63	1.00214	
2536	geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [source:swissprot;acc:o95749]	236.51	236.008	1.00213	
2537	vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [source:swissprot;acc:q9nrw7]	215.964	216.421	1.00212	
2538	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [source:swissprot;acc:p23246]	190.765	191.163	1.00209	
2539	gc-rich sequence dna-binding factor homolog. [source:swissprot;acc:q9y5b6]	217.144	216.699	1.00205	
2540	toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [source:swissprot;acc:o60603]	217.144	216.699	1.00205	
2541	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [source:swissprot;acc:p14868]	194.505	194.902	1.00204	
2542	p29ing4; candidate tumor suppressor p33 ing1 homolog. [source:refseq;acc:nm_016162]	218.068	217.633	1.002	
2543	tubulin tyrosine ligase-like protein hottl (hqp0207). [source:swissprot;acc:q9y4r7]	224.726	225.164	1.00195	
2544	aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [source:swissprot;acc:p48728]	212.67	212.262	1.00192	
2545	proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [source:swissprot;acc:p28065]	213.494	213.088	1.00191	
2546	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [source:refseq;acc:nm_015975]	197.138	197.507	1.00187	
2547	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14410]	206.894	206.51	1.00186	
2548	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14409]	206.899	206.516	1.00185	
2549	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:p32189]	206.902	206.519	1.00185	
2550	epsin 2 isoform b; eps15 binding protein. [source:refseq;acc:nm_014964]	217.587	217.988	1.00184	
2551	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	209.766	210.148	1.00182	
2552	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	193.12	193.467	1.0018	
2553	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [source:refseq;acc:nm_004824]	193.12	193.467	1.0018	
2554	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	193.12	193.467	1.0018	
2555	s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [source:swissprot;acc:p31153]	212.953	212.572	1.00179	
2556	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	193.119	193.46	1.00177	
2557	elongation factor 2 (ef-2). [source:swissprot;acc:p13639]	222.658	223.047	1.00175	
2558	metabotropic glutamate receptor 2 precursor (mglur2). [source:swissprot;acc:q14416]	222.658	223.047	1.00175	
2559	metabotropic glutamate receptor 3 precursor (mglur3). [source:swissprot;acc:q14832]	222.658	223.047	1.00175	
2560	monoglyceride lipase; lysophospholipase-like. [source:refseq;acc:nm_007283]	202.395	202.042	1.00175	
2561	fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:p09467]	209.825	210.18	1.00169	
2562	glycogenin-1 (ec 2.4.1.186). [source:swissprot;acc:p46976]	208.429	208.779	1.00168	
2563	adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [source:swissprot;acc:p55263]	208.429	208.779	1.00168	
2564	protein x 0001. [source:refseq;acc:nm_016302]	208.429	208.779	1.00168	
2565	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [source:swissprot;acc:o15488]	208.429	208.779	1.00168	
2566	serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [source:swissprot;acc:q96gd4]	219.907	220.267	1.00164	
2567	kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [source:swissprot;acc:q02241]	219.907	220.267	1.00164	
2568	serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [source:swissprot;acc:q9uqb9]	219.907	220.267	1.00164	
2569	serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [source:swissprot;acc:o14965]	219.907	220.267	1.00164	
2570	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [source:refseq;acc:nm_015247]	219.907	220.267	1.00164	
2571	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	209.549	209.205	1.00164	
2572	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [source:swissprot;acc:q16514]	203.953	204.285	1.00163	
2573	peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [source:swissprot;acc:q13162]	213.347	213.005	1.00161	
2574	swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [source:refseq;acc:nm_003074]	220.016	219.667	1.00159	
2575	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [source:swissprot;acc:p17706]	209.583	209.255	1.00157	
2576	beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [source:swissprot;acc:q13884]	213.422	213.75	1.00154	
2577	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	192.625	192.922	1.00154	
2578	beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [source:swissprot;acc:q13425]	213.422	213.75	1.00154	
2579	nitrilase 1. [source:refseq;acc:nm_005600]	213.422	213.75	1.00154	

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/