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

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Showing element 1268 to 1317 of 3228 in total

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

description	Rank	network_comparison	red	green
high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	2989	1	0.00001	0.00001
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	3144
high mobility group protein 2 (hmg-2). [swissprot;acc:p26583]	2856
high mobility group protein 4 (hmg-4) (high mobility group protein 2a) (hmg-2a). [swissprot;acc:o15347]	3203
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	2787
high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083]	2876
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	2863
high-mobility group 20a. [refseq;acc:nm_018200]	125	1.21429	208.588	171.778
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	1.21519	208.52	171.595
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	440	1.07843	231.802	249.983
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	788	1.04653	138.705	132.538
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357]	2169	1.00673	215.925	214.481
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	1715	1.01327	206.549	203.844
histidine-rich membrane protein ke4. [swissprot;acc:q92504]	2718	1.00052	216.52	216.632
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	1920	1.01013	187.292	185.413
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	1919	1.01015	187.231	185.349
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	182	1.15422	277.546	240.461
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	279	1.10605	252.644	228.42
histone deacetylase 1 (hd1). [swissprot;acc:q13547]	777	1.04853	225.989	215.53
histone deacetylase 11 (hd11). [swissprot;acc:q96db2]	2376	1.004	212.724	213.574
histone deacetylase 2 (hd2). [swissprot;acc:q92769]	775	1.04854	226.003	215.541
histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]	2813	1	0.00001	0.00001
histone deacetylase 4 (hd4). [swissprot;acc:p56524]	2424	1.00358	220.682	221.472
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6]	2423			221.471
histone deacetylase 6 (hd6). [swissprot;acc:q9ubn7]	3152	1	0.00001	0.00001
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]	2425	1.00358	220.682	221.472
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]	2784	1	0.00001	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	1.0601	247.47	233.441
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	1.05274	244.842	232.577
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	611	1.0601	247.47	233.441
histone h4. [swissprot;acc:p02304]	946	1.03576	227.765	219.902
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	1.02234	226.433	231.491
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	1.05938	217.67	230.596
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	1503	1.01828	242.181	237.834
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]	643	1.05938	217.67	230.596
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	1.0157	182.378	185.241
hmg2 like. [refseq;acc:nm_145205]	2799	1	0.00001	0.00001
homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786]	2194	1.00662	209.54	208.162

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.