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

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Showing element 1280 to 1329 of 3228 in total

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

description	Rank	green	network_comparison	red
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	1715	203.844	1.01327	206.549
histidine-rich membrane protein ke4. [swissprot;acc:q92504]	2718	216.632	1.00052	216.52
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	1920	185.413	1.01013	187.292
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	1919	185.349	1.01015	187.231
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	182	240.461	1.15422	277.546
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	279	228.42	1.10605	252.644
histone deacetylase 1 (hd1). [swissprot;acc:q13547]	777	215.53	1.04853	225.989
histone deacetylase 11 (hd11). [swissprot;acc:q96db2]	2376	213.574	1.004	212.724
histone deacetylase 2 (hd2). [swissprot;acc:q92769]	775	215.541	1.04854	226.003
histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]	2813	0.00001	1	0.00001
histone deacetylase 4 (hd4). [swissprot;acc:p56524]	2424	221.472	1.00358	220.682
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6]	2423	221.471
histone deacetylase 6 (hd6). [swissprot;acc:q9ubn7]	3152	0.00001	1	0.00001
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]	2425	221.472	1.00358	220.682
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]	2784	0.00001	1	0.00001
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	2767
histone h2a.e (h2a/e). [swissprot;acc:q99878]	2765
histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]	2769
histone h2a.x (h2a/x). [swissprot;acc:p16104]	2768
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]	2852
histone h2b. [refseq;acc:nm_175055]	608	233.441	1.0601	247.47
histone h2b.c (h2b/c). [swissprot;acc:q99880]	605
histone h2b.d (h2b/d). [swissprot;acc:q99877]	610
histone h2b.e (h2b/e). [swissprot;acc:q99879]	613
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	606
histone h2b.s (h2b/s). [swissprot;acc:p57053]	609
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	607
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	723	232.577	1.05274	244.842
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	611	233.441	1.0601	247.47
histone h4. [swissprot;acc:p02304]	946	219.902	1.03576	227.765
histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463]	1342	231.491	1.02234	226.433
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1]	1340
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]	645	230.596	1.05938	217.67
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	1503	237.834	1.01828	242.181
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]	643	230.596	1.05938	217.67
hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410]	1613	185.241	1.0157	182.378
hmg2 like. [refseq;acc:nm_145205]	2799	0.00001	1	0.00001
homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786]	2194	208.162	1.00662	209.54
homeobox protein barh-like 1. [swissprot;acc:q9hbu1]	582	252.492	1.06411	237.28
homeobox protein barh-like 2. [swissprot;acc:q9umq3]	587
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	557	194.371	1.06637	207.272
homeobox protein dlx-2. [swissprot;acc:q07687]	2337	230.294	1.00452	229.258
homeobox protein dlx-3. [swissprot;acc:o60479]	2340
homeobox protein dlx-5. [swissprot;acc:p56178]	2338
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622]	1167	213.784	1.02626	219.399
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	7	322	1.49767	215
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	614	202.125	1.06002	214.257
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	686	125.389	1.05602	132.413
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	685
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	616	202.132	1.05999	214.257

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.