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

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Showing element 1858 to 1907 of 3228 in total

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

description	Rank	red	green	network_comparison
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
nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838]	1734	221.921	219.081	1.01296
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3]	1127	239.219	232.837	1.02741
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	719	247.769	235.074	1.054
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	934	242.024	233.544	1.03631
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	170	227.199	192.715	1.17894
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	171	227.202	192.823	1.17829
nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748]	2785	0.00001	0.00001	1
nucleoplasmin 3. [swissprot;acc:o75607]	3096
nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [swissprot;acc:q9ukx7]	3154
nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]	1671	228.496	231.729	1.01415
nucleoporin like 1. [refseq;acc:nm_014089]	1776	216.878	214.286	1.0121
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	1826	202.393	200.094	1.01149
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	639	217.67	230.596	1.05938
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	1827	191.39	189.219	1.01147
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531]	1797	193.111	190.834	1.01193
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392]	1794	193.138	190.861
nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]	2757	0.00001	0.00001	1
nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]	2758
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	3080
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	518	250.858	234.563	1.06947
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	672	210.739	199.398	1.05688
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	671
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	370	242.159	265.104	1.09475
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	968	211.987	204.964	1.03426
numb-like protein (numb-r). [swissprot;acc:q9y6r0]	972
ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]	2045	199.928	198.24	1.00851

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.