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	Gene	Value Type	description	Rank	network_comparison	Filtered	green	Interaction Map	red

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Showing element 1818 to 1867 of 3228 in total

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

description	Rank	network_comparison	green	red
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]	1272	1.02425	167.177	171.231
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	267.226	248.152
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610]	1367	1.02194	228.799	223.887
neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]	2484	1.00287	218.72	218.093
neuronal shc. [refseq;acc:nm_016848]	2127	1.00696	222.788	221.248
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]	2336	1.00452	230.294	229.258
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	481	1.07405	254.667	237.109
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]	480
neurotrimin precursor (hnt). [swissprot;acc:q9p121]	1498	1.01863	219.924	224.022
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	1649	1.01445	215.942	219.062
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837]	1419	1.02084	208.229	203.979
nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]	2616	1.00139	202.54	202.821
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	201.674	201.452
nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221]	2651	1.00111	201.594	201.37
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	225.185	228.611
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177]	2301	1.00509	218.498	217.392
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274]	2257	1.00591	211.315	212.563
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	2649	1.00114	213.874	213.63
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	2499	1.00283	230.76	231.414
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	213.75	213.422
nitrogen fixation cluster-like. [refseq;acc:nm_014301]	1269	1.02425	167.177	171.231
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	234.401	250.538
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	212.404	221.965
nostrin. [refseq;acc:nm_052946]	162	1.19058	249.187	209.299
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	212.41	237.302
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	42.3003	50.7983
nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289]	2743	1.00022	198.321	198.278
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	201.674	201.452
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		201.673	201.451
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	212.142	214.234
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	225.185	228.611
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570]	2135	1.00696	206.308	207.743
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	151.009	151.386
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	531	1.06793	209.149	223.356
nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658]	3008	1	0.00001	0.00001
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]	997	1.03345	212.547	219.656
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]	1576	1.01645	218.982	222.585
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	690	1.05553	208.987	220.593
nuclear protein ukp68. [refseq;acc:nm_024824]	194	1.14055	199.458	227.491

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.