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

Results: HTML CSV LaTeX

Showing element 1813 to 1862 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence

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

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.