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	Network Comparison Type	description	Rank	Filtered	Interaction Map	network_comparison	green	red

Results: HTML CSV LaTeX

Showing element 1901 to 1950 of 3228 in total

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

description	Rank	network_comparison	green	red
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	518	1.06947	234.563	250.858
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	672	1.05688	199.398	210.739
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	265.104	242.159
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	968	1.03426	204.964	211.987
numb-like protein (numb-r). [swissprot;acc:q9y6r0]	972
ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]	2045	1.00851	198.24	199.928
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590]	1205	1.02533	219.251	224.805
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807]	1717	1.01327	218.164	221.058
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	184	1.15239	237.79	274.027
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	224	1.12285	165.623	185.969
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	251	1.11707	166.661	186.172
oligophrenin 1. [swissprot;acc:o60890]	504	1.07112	255.68	238.704
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	213.703	211.633
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	255	1.11569	179.88	200.691
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982]	1492	1.01883	220.017	224.159
opsin 4 (melanopsin). [swissprot;acc:q9uhm6]	583	1.06411	252.492	237.28
origin recognition complex subunit 2. [swissprot;acc:q13416]	3047	1	0.00001	0.00001
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	1.01272	222.215	219.423
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480]	1933	1.00998	217.82	215.667
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	2063	1.00833	205.923	207.638
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	2052	1.00834	205.95	207.667
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	2054		205.948	207.665
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736]	2133	1.00696	206.305	207.74
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	1544	1.01704	216.081	219.762
orphan nuclear receptor nr5a2 (alpha-1-fetoprotein transcription factor) (hepatocytic transcription factor) (b1-binding factor) (hb1f) (cyp7a promoter binding factor). [swissprot;acc:o00482]	3042	1	0.00001	0.00001
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	1406	1.021	208.456	212.833
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354]	2141	1.00689	206.343	207.765
orphan nuclear receptor tr2. [swissprot;acc:p13056]	1545	1.01702	216.083	219.76
osteoclast stimulating factor 1. [swissprot;acc:q92882]	759	1.04952	243.289	231.809
ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830]	2136	1.00696	222.788	221.248
oxidation resistance 1. [refseq;acc:nm_181354]	2051	1.00834	216.981	218.79
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133]	2422	1.00359	218.984	218.2
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055]	2416
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671]	1308	1.02343	213.439	218.44
p10-binding protein. [refseq;acc:nm_024491]	1611	1.01577	217.877	221.313
p28 ing5. [refseq;acc:nm_032329]	1917	1.01015	218.039	215.848
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162]	2542	1.002	217.633	218.068
p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831]	2733	1.00028	202.172	202.229
p47 protein isoform a. [refseq;acc:nm_016143]	2201	1.00654	212.254	213.642
p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44]	2752	1.00007	221.716	221.7
p66 alpha. [refseq;acc:nm_017660]	1560	1.01651	170.455	167.687
paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367]	1844	1.01109	212.417	214.773
pak1 interacting protein 1; pak1-interacting protein; pak/plc-interacting protein 1. [refseq;acc:nm_017906]	3072	1	0.00001	0.00001
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	213	1.127	186.95	210.693
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]	807	1.04425	221.785	212.386
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	199	1.13729	276.059	242.735
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	24	1.31818	44	58

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.