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	Filtered	Interaction Map	network_comparison	red	green

Results: HTML CSV LaTeX

Showing element 1868 to 1917 of 3228 in total

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

description	Rank	network_comparison	red	green
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	2521	1.00234	201.96	201.488
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]	2059	1.00834	218.79	216.981
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	1123	1.0275	169.031	164.507
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	1118	1.02753	168.995	164.467
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	1117	1.02754	168.989	164.46
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	1.10368	251.679	228.037
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	1.27519	260.532	204.309
nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662]	3113	1	0.00001	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	1.00095	208.438	208.635
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	1877	1.01075	212.186	214.467
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	1.07184	251.83	234.951
nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [swissprot;acc:q14978]	2842	1	0.00001	0.00001
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	479	1.07409	228.051	212.321
nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838]	1734	1.01296	221.921	219.081
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3]	1127	1.02741	239.219	232.837
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	719	1.054	247.769	235.074
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	934	1.03631	242.024	233.544
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	170	1.17894	227.199	192.715
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	171	1.17829	227.202	192.823
nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748]	2785	1	0.00001	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	1.01415	228.496	231.729
nucleoporin like 1. [refseq;acc:nm_014089]	1776	1.0121	216.878	214.286
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	1826	1.01149	202.393	200.094
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	639	1.05938	217.67	230.596
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	1827	1.01147	191.39	189.219
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	1.01193	193.111	190.834
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	1	0.00001	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
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	518	1.06947	250.858	234.563
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	672	1.05688	210.739	199.398
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	671
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	370	1.09475	242.159	265.104
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	968	1.03426	211.987	204.964
numb-like protein (numb-r). [swissprot;acc:q9y6r0]	972
ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]	2045	1.00851	199.928	198.24
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590]	1205	1.02533	224.805	219.251
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807]	1717	1.01327	221.058	218.164
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	184	1.15239	274.027	237.79
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	224	1.12285	185.969	165.623
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	251	1.11707	186.172	166.661
oligophrenin 1. [swissprot;acc:o60890]	504	1.07112	238.704	255.68
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]	502
oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8]	1966	1.00978	211.633	213.703
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	255	1.11569	200.691	179.88
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982]	1492	1.01883	224.159	220.017

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.