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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1850 to 1899 of 3228 in total

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

description	Rank	red	green	network_comparison
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
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

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.