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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Gene description Rank Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1813 to 1862 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

description	Rank	red	green	network_comparison	
neuromedin u receptor 2. [source:refseq;acc:nm_020167]	2991	0.00001	0.00001	1	
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	444	223.801	207.549	1.0783	
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	443	223.79	207.539	1.0783	
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	445	223.801	207.549	1.0783	
neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [source:swissprot;acc:p32076]	1183	225.103	230.928	1.02588	
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [source:swissprot;acc:q15822]	1272	171.231	167.177	1.02425	
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [source:swissprot;acc:p32297]	1276	171.231	167.177	1.02425	
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [source:swissprot;acc:p43681]	1275	171.231	167.177	1.02425	
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [source:swissprot;acc:q15825]	1268	171.231	167.177	1.02425	
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	465	248.152	267.226	1.07686	
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [source:swissprot;acc:p36610]	1367	223.887	228.799	1.02194	
neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [source:swissprot;acc:q12840]	2484	218.093	218.72	1.00287	
neuronal shc. [source:refseq;acc:nm_016848]	2127	221.248	222.788	1.00696	
neuronal tropomodulin (n-tmod) (tropomodulin 2). [source:swissprot;acc:q9nzr1]	2336	229.258	230.294	1.00452	
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	481	237.109	254.667	1.07405	
neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	480	237.109	254.667	1.07405	
neurotrimin precursor (hnt). [source:swissprot;acc:q9p121]	1498	224.022	219.924	1.01863	
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [source:swissprot;acc:p56730]	1649	219.062	215.942	1.01445	
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	1419	203.979	208.229	1.02084	
nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [source:swissprot;acc:p25963]	2616	202.821	202.54	1.00139	
nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [source:swissprot;acc:q15653]	2653	201.452	201.674	1.0011	
nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [source:swissprot;acc:o00221]	2651	201.37	201.594	1.00111	
ngd5 protein homolog (cgi-53). [source:swissprot;acc:q9y366]	3133	0.00001	0.00001	1	
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [source:swissprot;acc:p55769]	1622	228.611	225.185	1.01521	
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [source:refseq;acc:nm_178177]	2301	217.392	218.498	1.00509	
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [source:swissprot;acc:q15274]	2257	212.563	211.315	1.00591	
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	2649	213.63	213.874	1.00114	
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [source:refseq;acc:nm_014062]	2499	231.414	230.76	1.00283	
nipsnap1 protein. [source:swissprot;acc:q9bpw8]	2770	0.00001	0.00001	1	
nipsnap2 protein (glioblastoma amplified sequence). [source:swissprot;acc:o75323]	2918	0.00001	0.00001	1	
nitrilase 1. [source:refseq;acc:nm_005600]	2579	213.422	213.75	1.00154	
nitrogen fixation cluster-like. [source:refseq;acc:nm_014301]	1269	171.231	167.177	1.02425	
nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [source:refseq;acc:nm_177400]	2909	0.00001	0.00001	1	
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	526	250.538	234.401	1.06884	
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [source:swissprot;acc:p22307]	800	221.965	212.404	1.04501	
nostrin. [source:refseq;acc:nm_052946]	162	209.299	249.187	1.19058	
nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [source:swissprot;acc:p48745]	2970	0.00001	0.00001	1	
ns1-associated protein 1. [source:refseq;acc:nm_006372]	249	237.302	212.41	1.11719	
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [source:swissprot;acc:p23497]	3184	0.00001	0.00001	1	
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	147	50.7983	42.3003	1.2009	
nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [source:refseq;acc:nm_004289]	2743	198.278	198.321	1.00022	
nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [source:swissprot;acc:q14494]	2742	198.278	198.321	1.00022	
nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [source:swissprot;acc:q00653]	2654	201.452	201.674	1.0011	
nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [source:swissprot;acc:p19838]	2652	201.451	201.673	1.0011	
nuclear factor related to kappa b binding protein. [source:refseq;acc:nm_006165]	2823	0.00001	0.00001	1	
nuclear factor, interleukin 3 regulated. [source:refseq;acc:nm_005384]	1946	214.234	212.142	1.00986	
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [source:refseq;acc:nm_012345]	1623	228.611	225.185	1.01521	
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [source:swissprot;acc:q92570]	2135	207.743	206.308	1.00696	
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [source:swissprot;acc:q12972]	2507	151.386	151.009	1.0025	
nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	531	223.356	209.149	1.06793	

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/