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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3508 to 3557 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1754	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [source:swissprot;acc:q9y617]	Divided	220.091	217.362	1.01256	
1755	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	Divided	180.609	178.393	1.01242	
1755	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [source:swissprot;acc:q99962]	Subtracted	206.522	203.818	2.704	
1756	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	Subtracted	215.673	212.971	2.702	
1756	megf6 (fragment). [source:sptrembl;acc:o75095]	Divided	221.811	219.09	1.01242	
1757	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [source:refseq;acc:nm_019857]	Divided	180.537	178.325	1.0124	
1757	similar to lim domain only 7 (fragment). [source:sptrembl;acc:q8n6m2]	Subtracted	216.27	213.57	2.7	
1758	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	Divided	233.45	230.595	1.01238	
1758	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	Subtracted	206.251	203.553	2.698	
1759	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]	Subtracted	221.082	223.778	2.696	
1759	ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [source:swissprot;acc:q9y265]	Divided	219.37	222.086	1.01238	
1760	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [source:swissprot;acc:p05976]	Divided	233.45	230.595	1.01238	
1760	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Subtracted	134.233	136.922	2.689	
1761	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	Subtracted	215.698	218.369	2.671	
1761	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [source:swissprot;acc:p08590]	Divided	233.45	230.595	1.01238	
1762	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [source:swissprot;acc:q9y234]	Subtracted	206.595	209.258	2.663	
1762	nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [source:swissprot;acc:o75380]	Divided	233.45	230.595	1.01238	
1763	myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [source:swissprot;acc:p14649]	Divided	233.45	230.595	1.01238	
1763	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [source:swissprot;acc:p23258]	Subtracted	206.595	209.258	2.663	
1764	defender against cell death 1 (dad-1). [source:swissprot;acc:p46966]	Subtracted	206.595	209.258	2.663	
1764	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	Divided	233.45	230.595	1.01238	
1765	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	Divided	215.698	218.369	1.01238	
1765	t-complex 11. [source:refseq;acc:nm_018679]	Subtracted	206.595	209.258	2.663	
1766	c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [source:swissprot;acc:p11586]	Divided	228.932	231.732	1.01223	
1766	tubulin gamma-2 chain (gamma-2 tubulin). [source:swissprot;acc:q9nrh3]	Subtracted	206.595	209.258	2.663	
1767	60s ribosomal protein l24 (l30). [source:swissprot;acc:p38663]	Divided	201.288	198.86	1.01221	
1767	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [source:swissprot;acc:q03014]	Subtracted	198.014	195.385	2.629	
1768	estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [source:swissprot;acc:p51659]	Divided	185.276	187.534	1.01219	
1768	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [source:swissprot;acc:p36776]	Subtracted	223.214	225.827	2.613	
1769	5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	Divided	223.016	225.734	1.01219	
1769	nucleoporin like 1. [source:refseq;acc:nm_014089]	Subtracted	216.878	214.286	2.592	
1770	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]	Divided	221.082	223.778	1.01219	
1770	rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [source:refseq;acc:nm_015320]	Subtracted	216.878	214.286	2.592	
1771	cdc42 guanine exchange factor 9; hpem-2 collybistin. [source:refseq;acc:nm_015185]	Subtracted	216.878	214.286	2.592	
1771	putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [source:swissprot;acc:q9uet6]	Divided	223.016	225.734	1.01219	
1772	dna mismatch repair protein mlh3 (mutl protein homolog 3). [source:swissprot;acc:q9uhc1]	Subtracted	206.058	203.485	2.573	
1772	spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [source:swissprot;acc:o15020]	Divided	223.032	225.739	1.01214	
1773	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [source:swissprot;acc:q14576]	Subtracted	217.866	215.295	2.571	
1773	spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [source:swissprot;acc:q01082]	Divided	223.032	225.739	1.01214	
1774	elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [source:swissprot;acc:p26378]	Subtracted	217.766	215.199	2.567	
1774	phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [source:swissprot;acc:o95394]	Divided	223.032	225.739	1.01214	
1775	elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [source:swissprot;acc:q12926]	Subtracted	217.724	215.158	2.566	
1775	serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [source:swissprot;acc:o15269]	Divided	207.757	210.274	1.01212	
1776	elav-like protein 1 (hu-antigen r) (hur). [source:swissprot;acc:q15717]	Subtracted	217.807	215.242	2.565	
1776	nucleoporin like 1. [source:refseq;acc:nm_014089]	Divided	216.878	214.286	1.0121	
1777	6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	Subtracted	240.317	242.881	2.564	
1777	rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [source:refseq;acc:nm_015320]	Divided	216.878	214.286	1.0121	
1778	cdc42 guanine exchange factor 9; hpem-2 collybistin. [source:refseq;acc:nm_015185]	Divided	216.878	214.286	1.0121	
1778	cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [source:swissprot;acc:q92879]	Subtracted	217.984	215.441	2.543	
1779	pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [source:swissprot;acc:p40424]	Divided	206.332	203.874	1.01206	

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/