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

Results: HTML CSV LaTeX

Showing element 1275 to 1324 of 3228 in total

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

description	Rank	red	green	network_comparison
high-mobility group 20a. [refseq;acc:nm_018200]	125	208.588	171.778	1.21429
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	124	208.52	171.595	1.21519
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	440	231.802	249.983	1.07843
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	788	138.705	132.538	1.04653
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357]	2169	215.925	214.481	1.00673
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	1715	206.549	203.844	1.01327
histidine-rich membrane protein ke4. [swissprot;acc:q92504]	2718	216.52	216.632	1.00052
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	1920	187.292	185.413	1.01013
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	1919	187.231	185.349	1.01015
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	182	277.546	240.461	1.15422
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	279	252.644	228.42	1.10605
histone deacetylase 1 (hd1). [swissprot;acc:q13547]	777	225.989	215.53	1.04853
histone deacetylase 11 (hd11). [swissprot;acc:q96db2]	2376	212.724	213.574	1.004
histone deacetylase 2 (hd2). [swissprot;acc:q92769]	775	226.003	215.541	1.04854
histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]	2813	0.00001	0.00001	1
histone deacetylase 4 (hd4). [swissprot;acc:p56524]	2424	220.682	221.472	1.00358
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6]	2423		221.471
histone deacetylase 6 (hd6). [swissprot;acc:q9ubn7]	3152	0.00001	0.00001	1
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]	2425	220.682	221.472	1.00358
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]	2784	0.00001	0.00001	1
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	247.47	233.441	1.0601
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	244.842	232.577	1.05274
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	611	247.47	233.441	1.0601
histone h4. [swissprot;acc:p02304]	946	227.765	219.902	1.03576
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	226.433	231.491	1.02234
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	217.67	230.596	1.05938
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	1503	242.181	237.834	1.01828
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]	643	217.67	230.596	1.05938
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	182.378	185.241	1.0157
hmg2 like. [refseq;acc:nm_145205]	2799	0.00001	0.00001	1
homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786]	2194	209.54	208.162	1.00662
homeobox protein barh-like 1. [swissprot;acc:q9hbu1]	582	237.28	252.492	1.06411
homeobox protein barh-like 2. [swissprot;acc:q9umq3]	587
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	557	207.272	194.371	1.06637
homeobox protein dlx-2. [swissprot;acc:q07687]	2337	229.258	230.294	1.00452
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	219.399	213.784	1.02626

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.