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

Results: HTML CSV LaTeX

Showing element 1832 to 1881 of 3228 in total

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

description	Rank	red	green	network_comparison
nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [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). [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). [swissprot;acc:o00221]	2651	201.37	201.594	1.00111
ngd5 protein homolog (cgi-53). [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). [swissprot;acc:p55769]	1622	228.611	225.185	1.01521
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [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). [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). [swissprot;acc:q9gzt8]	2649	213.63	213.874	1.00114
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	2499	231.414	230.76	1.00283
nipsnap1 protein. [swissprot;acc:q9bpw8]	2770	0.00001	0.00001	1
nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323]	2918
nitrilase 1. [refseq;acc:nm_005600]	2579	213.422	213.75	1.00154
nitrogen fixation cluster-like. [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. [refseq;acc:nm_177400]	2909	0.00001	0.00001	1
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [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). [swissprot;acc:p22307]	800	221.965	212.404	1.04501
nostrin. [refseq;acc:nm_052946]	162	209.299	249.187	1.19058
nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [swissprot;acc:p48745]	2970	0.00001	0.00001	1
ns1-associated protein 1. [refseq;acc:nm_006372]	249	237.302	212.41	1.11719
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	3184	0.00001	0.00001	1
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	147	50.7983	42.3003	1.2009
nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [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). [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	201.452	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]. [swissprot;acc:p19838]	2652	201.451	201.673
nuclear factor related to kappa b binding protein. [refseq;acc:nm_006165]	2823	0.00001	0.00001	1
nuclear factor, interleukin 3 regulated. [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. [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). [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)]. [swissprot;acc:q12972]	2507	151.386	151.009	1.0025
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	531	223.356	209.149	1.06793
nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658]	3008	0.00001	0.00001	1
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]	997	219.656	212.547	1.03345
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]	1576	222.585	218.982	1.01645
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	690	220.593	208.987	1.05553
nuclear protein ukp68. [refseq;acc:nm_024824]	194	227.491	199.458	1.14055
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	2521	201.96	201.488	1.00234
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]	2059	218.79	216.981	1.00834
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	1123	169.031	164.507	1.0275
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	1118	168.995	164.467	1.02753
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	1117	168.989	164.46	1.02754
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	251.679	228.037	1.10368
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	260.532	204.309	1.27519
nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662]	3113	0.00001	0.00001	1
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	208.438	208.635	1.00095
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	1877	212.186	214.467	1.01075
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	251.83	234.951	1.07184
nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [swissprot;acc:q14978]	2842	0.00001	0.00001	1
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	479	228.051	212.321	1.07409

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.