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 1880 to 1929 of 3228 in total

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

description	Rank	red	green	network_comparison
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
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590]	1205	224.805	219.251	1.02533
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807]	1717	221.058	218.164	1.01327
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	184	274.027	237.79	1.15239
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	224	185.969	165.623	1.12285
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	251	186.172	166.661	1.11707
oligophrenin 1. [swissprot;acc:o60890]	504	238.704	255.68	1.07112
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	211.633	213.703	1.00978
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	255	200.691	179.88	1.11569
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982]	1492	224.159	220.017	1.01883
opsin 4 (melanopsin). [swissprot;acc:q9uhm6]	583	237.28	252.492	1.06411
origin recognition complex subunit 2. [swissprot;acc:q13416]	3047	0.00001	0.00001	1
origin recognition complex subunit 5. [swissprot;acc:o43913]	2851
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181]	1746	219.423	222.215	1.01272
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480]	1933	215.667	217.82	1.00998
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	2063	207.638	205.923	1.00833
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	2052	207.667	205.95	1.00834
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	2054	207.665	205.948
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736]	2133	207.74	206.305	1.00696
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	1544	219.762	216.081	1.01704
orphan nuclear receptor nr5a2 (alpha-1-fetoprotein transcription factor) (hepatocytic transcription factor) (b1-binding factor) (hb1f) (cyp7a promoter binding factor). [swissprot;acc:o00482]	3042	0.00001	0.00001	1
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	1406	212.833	208.456	1.021

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.