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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Value Type Interaction Map description Network Comparison Type Rank Gene red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1332 to 1381 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	574	6739.61	7644.58	1.13428	
homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	337	20446.1	24136.4	1.18049	
homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	339	20446.1	24136.4	1.18049	
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	340	20446.1	24136.4	1.18049	
homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	576	6739.7	7644.6	1.13426	
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	341	20446.1	24136.4	1.18049	
homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	591	6740.5	7644.76	1.13415	
homeobox protein meis1. [source:swissprot;acc:o00470]	2469	7765.3	8004	1.03074	
homeobox protein meis2 (meis1-related protein 1). [source:swissprot;acc:o14770]	2470	7765.3	8004	1.03074	
homeobox protein meis3 (meis1-related protein 2) (fragment). [source:swissprot;acc:q99687]	2474	7765.3	8004	1.03074	
homeobox protein nkx-6.1. [source:swissprot;acc:p78426]	2859	0.00001	0.00001	1	
homeobox protein otx1. [source:swissprot;acc:p32242]	2399	5691.1	5913.92	1.03915	
homeobox protein otx2. [source:swissprot;acc:p32243]	2395	5682	5905.08	1.03926	
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [source:swissprot;acc:q03014]	2454	8751.01	8480.03	1.03196	
homeobox protein six1 (sine oculis homeobox homolog 1). [source:swissprot;acc:q15475]	1704	5778.4	6176.13	1.06883	
homeobox protein six2 (sine oculis homeobox homolog 2). [source:swissprot;acc:q9npc8]	1709	5775.55	6171.79	1.06861	
homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	245	4251.65	5212.33	1.22595	
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	243	4246.95	5208.98	1.22652	
homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	246	4252.66	5213.05	1.22583	
homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [source:swissprot;acc:q15011]	3196	0.00001	0.00001	1	
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	3053	0.00001	0.00001	1	
homolog of yeast maf1. [source:refseq;acc:nm_032272]	1097	6133.83	6690.18	1.0907	
hormone sensitive lipase (ec 3.1.1.-) (hsl). [source:swissprot;acc:q05469]	3172	0.00001	0.00001	1	
hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	2746	4188.5	4194.22	1.00137	
hrd1 protein isoform a; synoviolin1. [source:refseq;acc:nm_032431]	1812	5514.19	5871.64	1.06482	
hsgcn1 (fragment). [source:sptrembl;acc:q99736]	1424	5628.53	6063.61	1.0773	
hskin17 protein. [source:refseq;acc:nm_012311]	1092	5791.05	6316.61	1.09075	
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [source:swissprot;acc:q16543]	1922	5567.41	5914.05	1.06226	
human immunodeficiency virus type i enhancer binding protein 3. [source:refseq;acc:nm_024503]	694	7725.1	8647.74	1.11943	
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [source:swissprot;acc:p31629]	696	7725.1	8647.74	1.11943	
huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	1250	10733.4	9902.6	1.0839	
huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	1256	10719	9891.08	1.0837	
huntingtin interacting protein c. [source:refseq;acc:nm_012272]	114	4300.47	5807.72	1.35048	
huntingtin interacting protein e; huntingtin interactor protein e. [source:refseq;acc:nm_007076]	2715	5332.98	5351.72	1.00351	
huntingtin-associated protein-interacting protein (duo protein). [source:swissprot;acc:o60229]	813	5641.11	6255.99	1.109	
huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	94	4247.86	5941.88	1.39879	
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	1689	5767.69	6165.87	1.06904	
hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [source:refseq;acc:nm_004507]	2107	6916.14	7295.24	1.05481	
hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [source:refseq;acc:nm_014282]	2108	6916.14	7295.24	1.05481	
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [source:swissprot;acc:q92839]	2012	5391.27	5706.64	1.0585	
hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [source:swissprot;acc:q92819]	2011	5391.27	5706.64	1.0585	
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [source:swissprot;acc:o00219]	2013	5391.27	5706.64	1.0585	
hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [source:swissprot;acc:q9ujm8]	2168	4561.75	4799.24	1.05206	
hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [source:swissprot;acc:q9nyq3]	2382	4457.6	4642.72	1.04153	
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [source:swissprot;acc:q16775]	2398	6707.29	6970.07	1.03918	
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [source:swissprot;acc:p46597]	1919	5444.6	5783.95	1.06233	
hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [source:swissprot;acc:q01581]	2303	6946.6	7263.68	1.04565	
hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [source:swissprot;acc:p54868]	2301	6946.6	7263.68	1.04565	
hyporthetical protein mgc27169. [source:refseq;acc:nm_176782]	2468	7765.3	8004	1.03074	
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	420	10235.2	11830.8	1.15589	

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/