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 - 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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2001 to 2050 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2001	dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [source:swissprot;acc:p33992]	5047.2	5344.68	1.05894	
2002	survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [source:swissprot;acc:o14893]	5047.2	5344.68	1.05894	
2003	probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [source:swissprot;acc:q9uhi6]	5047.2	5344.68	1.05894	
2004	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [source:swissprot;acc:q9y690]	5047.87	5344.95	1.05885	
2005	atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [source:swissprot;acc:p53396]	6064.92	6421.65	1.05882	
2006	transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [source:swissprot;acc:q15014]	5048.26	5345.1	1.0588	
2007	adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [source:swissprot;acc:q9bxs5]	5684.61	6018.72	1.05877	
2008	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	3637.47	3435.61	1.05876	
2009	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [source:swissprot;acc:q05932]	4934.48	5223.69	1.05861	
2010	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [source:swissprot;acc:q9y6q5]	5671.62	6003.67	1.05855	
2011	hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [source:swissprot;acc:q92819]	5391.27	5706.64	1.0585	
2012	hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [source:swissprot;acc:q92839]	5391.27	5706.64	1.0585	
2013	hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [source:swissprot;acc:o00219]	5391.27	5706.64	1.0585	
2014	kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [source:swissprot;acc:o15066]	5934.08	6281.2	1.0585	
2015	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [source:sptrembl;acc:q9uge0]	6555.42	6938.82	1.05849	
2016	lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [source:swissprot;acc:q04760]	6555.42	6938.82	1.05849	
2017	lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [source:refseq;acc:nm_006330]	6555.42	6938.82	1.05849	
2018	mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [source:swissprot;acc:p30039]	6555.42	6938.82	1.05849	
2019	lysophospholipase ii; acyl-protein thioesterase. [source:refseq;acc:nm_007260]	6555.42	6938.82	1.05849	
2020	diphthamide biosynthesis-like protein 2. [source:refseq;acc:nm_001384]	4935.84	5224.27	1.05844	
2021	kinesin-like protein kif3c. [source:swissprot;acc:o14782]	5934.68	6281.49	1.05844	
2022	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [source:refseq;acc:nm_014666]	5520.26	5841.16	1.05813	
2023	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	3560.24	3364.84	1.05807	
2024	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [source:swissprot;acc:o15392]	5976.81	6323.87	1.05807	
2025	candidate tumor suppressor in ovarian cancer 2. [source:refseq;acc:nm_080822]	4813.13	5091.36	1.05781	
2026	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [source:swissprot;acc:p14868]	6766.45	7155.54	1.0575	
2027	rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [source:refseq;acc:nm_004584]	6218.34	6575.81	1.05749	
2028	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	10243.4	9686.82	1.05746	
2029	paraspeckle protein 1. [source:refseq;acc:nm_018282]	10241.3	9685.21	1.05742	
2030	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]	5060.82	5350.93	1.05732	
2031	eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [source:swissprot;acc:p05198]	5060.82	5350.93	1.05732	
2032	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]	5060.82	5350.93	1.05732	
2033	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	6101.12	6449.87	1.05716	
2034	topoisomerase (dna) ii binding protein. [source:refseq;acc:nm_007027]	6920.71	7315.59	1.05706	
2035	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [source:swissprot;acc:q15067]	6920.71	7315.59	1.05706	
2036	atp synthase f chain, mitochondrial (ec 3.6.3.14). [source:swissprot;acc:p56134]	6920.71	7315.59	1.05706	
2037	probable atp-dependent helicase ddx35 (deah-box protein 35). [source:swissprot;acc:q9h5z1]	6920.71	7315.59	1.05706	
2038	transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [source:swissprot;acc:p49848]	7088.08	7492.23	1.05702	
2039	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	3646.01	3449.54	1.05696	
2040	rho-gtpase-activating protein 8. [source:swissprot;acc:q9nsg0]	6036.68	6379.44	1.05678	
2041	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [source:swissprot;acc:q07960]	6036.68	6379.44	1.05678	
2042	kinesin light chain 2 (klc 2). [source:swissprot;acc:q9h0b6]	6036.62	6379.38	1.05678	
2043	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [source:swissprot;acc:p33176]	6036.68	6379.44	1.05678	
2044	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [source:swissprot;acc:o60282]	6036.68	6379.44	1.05678	
2045	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [source:swissprot;acc:q12840]	6036.68	6379.44	1.05678	
2046	kinesin light chain 1 (klc 1). [source:swissprot;acc:q07866]	6036.73	6379.48	1.05678	
2047	transcription factor iiia (factor a) (tfiiia). [source:swissprot;acc:q92664]	6036.68	6379.44	1.05678	
2048	exocyst complex component sec3 (bm-012). [source:swissprot;acc:q9nv70]	6036.68	6379.44	1.05678	
2049	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [source:refseq;acc:nm_003075]	5634.94	5953.19	1.05648	
2050	adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [source:swissprot;acc:p21851]	5556.36	5870.11	1.05647	

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/