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	green	network_comparison	Filtered	red	Interaction Map

Results: HTML CSV LaTeX

Showing element 1830 to 1879 of 3228 in total

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

description	Rank	green	network_comparison	red
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	1649	215.942	1.01445	219.062
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837]	1419	208.229	1.02084	203.979
nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]	2616	202.54	1.00139	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	201.674	1.0011	201.452
nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221]	2651	201.594	1.00111	201.37
ngd5 protein homolog (cgi-53). [swissprot;acc:q9y366]	3133	0.00001	1	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	225.185	1.01521	228.611
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177]	2301	218.498	1.00509	217.392
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274]	2257	211.315	1.00591	212.563
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	2649	213.874	1.00114	213.63
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	2499	230.76	1.00283	231.414
nipsnap1 protein. [swissprot;acc:q9bpw8]	2770	0.00001	1	0.00001
nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323]	2918
nitrilase 1. [refseq;acc:nm_005600]	2579	213.75	1.00154	213.422
nitrogen fixation cluster-like. [refseq;acc:nm_014301]	1269	167.177	1.02425	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	0.00001	1	0.00001
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	526	234.401	1.06884	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	212.404	1.04501	221.965
nostrin. [refseq;acc:nm_052946]	162	249.187	1.19058	209.299
nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [swissprot;acc:p48745]	2970	0.00001	1	0.00001
ns1-associated protein 1. [refseq;acc:nm_006372]	249	212.41	1.11719	237.302
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	3184	0.00001	1	0.00001
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	147	42.3003	1.2009	50.7983
nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289]	2743	198.321	1.00022	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	201.674	1.0011	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	0.00001	1	0.00001
nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384]	1946	212.142	1.00986	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	225.185	1.01521	228.611
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570]	2135	206.308	1.00696	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	151.009	1.0025	151.386
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	531	209.149	1.06793	223.356
nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658]	3008	0.00001	1	0.00001
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]	997	212.547	1.03345	219.656
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]	1576	218.982	1.01645	222.585
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	690	208.987	1.05553	220.593
nuclear protein ukp68. [refseq;acc:nm_024824]	194	199.458	1.14055	227.491
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	2521	201.488	1.00234	201.96
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]	2059	216.981	1.00834	218.79
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	1123	164.507	1.0275	169.031
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	1118	164.467	1.02753	168.995
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	1117	164.46	1.02754	168.989
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	291	228.037	1.10368	251.679
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	35	204.309	1.27519	260.532
nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662]	3113	0.00001	1	0.00001
nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991]	2683	208.635	1.00095	208.438
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	1877	214.467	1.01075	212.186
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303]	1879
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	491	234.951	1.07184	251.83

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.