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

Results: HTML CSV LaTeX

Showing element 1851 to 1900 of 3228 in total

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

description	Rank	green	network_comparison	red
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
nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [swissprot;acc:q14978]	2842	0.00001	1	0.00001
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	479	212.321	1.07409	228.051
nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838]	1734	219.081	1.01296	221.921
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3]	1127	232.837	1.02741	239.219
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	719	235.074	1.054	247.769
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	934	233.544	1.03631	242.024
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	170	192.715	1.17894	227.199
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	171	192.823	1.17829	227.202
nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748]	2785	0.00001	1	0.00001
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	231.729	1.01415	228.496
nucleoporin like 1. [refseq;acc:nm_014089]	1776	214.286	1.0121	216.878
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	1826	200.094	1.01149	202.393
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	639	230.596	1.05938	217.67
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	1827	189.219	1.01147	191.39
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	190.834	1.01193	193.111
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	190.861		193.138
nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]	2757	0.00001	1	0.00001
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

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.