Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 description Rank Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1277 to 1326 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

description	Rank	red	green	network_comparison	
highly expressed in cancer, rich in leucine heptad repeats. [source:refseq;acc:nm_006101]	440	231.802	249.983	1.07843	
hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	788	138.705	132.538	1.04653	
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [source:swissprot;acc:p42357]	2169	215.925	214.481	1.00673	
histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	1715	206.549	203.844	1.01327	
histidine-rich membrane protein ke4. [source:swissprot;acc:q92504]	2718	216.52	216.632	1.00052	
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	1920	187.292	185.413	1.01013	
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	1919	187.231	185.349	1.01015	
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source: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). [source:swissprot;acc:q16576]	279	252.644	228.42	1.10605	
histone deacetylase 1 (hd1). [source:swissprot;acc:q13547]	777	225.989	215.53	1.04853	
histone deacetylase 11 (hd11). [source:swissprot;acc:q96db2]	2376	212.724	213.574	1.004	
histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	775	226.003	215.541	1.04854	
histone deacetylase 3 (hd3) (rpd3-2). [source:swissprot;acc:o15379]	2813	0.00001	0.00001	1	
histone deacetylase 4 (hd4). [source:swissprot;acc:p56524]	2424	220.682	221.472	1.00358	
histone deacetylase 5 (hd5) (antigen ny-co-9). [source:swissprot;acc:q9uql6]	2423	220.682	221.471	1.00358	
histone deacetylase 6 (hd6). [source:swissprot;acc:q9ubn7]	3152	0.00001	0.00001	1	
histone deacetylase 9 (hd9) (hd7b) (hd7). [source:swissprot;acc:q9ukv0]	2425	220.682	221.472	1.00358	
histone h2a.a (h2a/a) (h2a.2). [source: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). [source:swissprot;acc:p02261]	2767	0.00001	0.00001	1	
histone h2a.e (h2a/e). [source:swissprot;acc:q99878]	2765	0.00001	0.00001	1	
histone h2a.q (h2a/q) (h2a-gl101) (fragment). [source:swissprot;acc:q16777]	2769	0.00001	0.00001	1	
histone h2a.x (h2a/x). [source:swissprot;acc:p16104]	2768	0.00001	0.00001	1	
histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	2852	0.00001	0.00001	1	
histone h2b. [source:refseq;acc:nm_175055]	608	247.47	233.441	1.0601	
histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	605	247.47	233.441	1.0601	
histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	610	247.47	233.441	1.0601	
histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	613	247.47	233.441	1.0601	
histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	606	247.47	233.441	1.0601	
histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	609	247.47	233.441	1.0601	
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	607	247.47	233.441	1.0601	
histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	723	244.842	232.577	1.05274	
histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	611	247.47	233.441	1.0601	
histone h4. [source: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). [source: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). [source:swissprot;acc:q9h5i1]	1340	226.433	231.491	1.02234	
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [source:refseq;acc:nm_014500]	645	217.67	230.596	1.05938	
hiv-1 rev binding protein 2; rev interacting protein. [source:refseq;acc:nm_007043]	1503	242.181	237.834	1.01828	
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [source: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. [source:refseq;acc:nm_006410]	1613	182.378	185.241	1.0157	
hmg2 like. [source:refseq;acc:nm_145205]	2799	0.00001	0.00001	1	
homeobox prospero-like protein prox1 (prox 1). [source:swissprot;acc:q92786]	2194	209.54	208.162	1.00662	
homeobox protein barh-like 1. [source:swissprot;acc:q9hbu1]	582	237.28	252.492	1.06411	
homeobox protein barh-like 2. [source:swissprot;acc:q9umq3]	587	237.28	252.492	1.06411	
homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	557	207.272	194.371	1.06637	
homeobox protein dlx-2. [source:swissprot;acc:q07687]	2337	229.258	230.294	1.00452	
homeobox protein dlx-3. [source:swissprot;acc:o60479]	2340	229.258	230.294	1.00452	
homeobox protein dlx-5. [source:swissprot;acc:p56178]	2338	229.258	230.294	1.00452	
homeobox protein engrailed-2 (hu-en-2). [source:swissprot;acc:p19622]	1167	219.399	213.784	1.02626	
homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	7	215	322	1.49767	
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	614	214.257	202.125	1.06002	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/