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 1725 to 1774 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1725	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [source:swissprot;acc:q9y4w6]	217.676	220.53	1.01311	
1726	alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [source:swissprot;acc:q9byc5]	217.676	220.53	1.01311	
1727	inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [source:swissprot;acc:p29218]	210.366	213.118	1.01308	
1728	inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [source:swissprot;acc:o14732]	210.358	213.103	1.01305	
1729	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	187.582	190.028	1.01304	
1730	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [source:swissprot;acc:q8ni60]	215.336	212.567	1.01303	
1731	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [source:refseq;acc:nm_052853]	215.336	212.567	1.01303	
1732	aarf domain containing kinase 4. [source:refseq;acc:nm_024876]	215.336	212.567	1.01303	
1733	aarf domain containing kinase 1. [source:refseq;acc:nm_020421]	215.336	212.567	1.01303	
1734	nucleolar protein family a, member 2; component of the h/aca snornp. [source:refseq;acc:nm_017838]	221.921	219.081	1.01296	
1735	leucyl-trna synthetase. [source:refseq;acc:nm_020117]	218.99	216.189	1.01296	
1736	transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [source:swissprot;acc:p35269]	221.921	219.081	1.01296	
1737	probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [source:swissprot;acc:q15031]	218.99	216.189	1.01296	
1738	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [source:swissprot;acc:q9y234]	206.595	209.258	1.01289	
1739	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [source:swissprot;acc:p23258]	206.595	209.258	1.01289	
1740	defender against cell death 1 (dad-1). [source:swissprot;acc:p46966]	206.595	209.258	1.01289	
1741	t-complex 11. [source:refseq;acc:nm_018679]	206.595	209.258	1.01289	
1742	tubulin gamma-2 chain (gamma-2 tubulin). [source:swissprot;acc:q9nrh3]	206.595	209.258	1.01289	
1743	pre-mrna cleavage factor i, 59 kda subunit. [source:refseq;acc:nm_024811]	218.176	215.402	1.01288	
1744	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [source:refseq;acc:nm_003901]	219.423	222.215	1.01272	
1745	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	219.423	222.215	1.01272	
1746	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [source:swissprot;acc:p04181]	219.423	222.215	1.01272	
1747	tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [source:swissprot;acc:p18074]	188.452	190.845	1.0127	
1748	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	215.673	212.971	1.01269	
1749	dna mismatch repair protein mlh3 (mutl protein homolog 3). [source:swissprot;acc:q9uhc1]	206.058	203.485	1.01264	
1750	similar to lim domain only 7 (fragment). [source:sptrembl;acc:q8n6m2]	216.27	213.57	1.01264	
1751	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]	221.185	223.97	1.01259	
1752	brca1-associated ring domain protein 1 (bard-1). [source:swissprot;acc:q99728]	216.271	218.991	1.01258	
1753	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [source:swissprot;acc:q9uj68]	220.091	217.362	1.01256	
1754	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [source:swissprot;acc:q9y617]	220.091	217.362	1.01256	
1755	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	180.609	178.393	1.01242	
1756	megf6 (fragment). [source:sptrembl;acc:o75095]	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]	180.537	178.325	1.0124	
1758	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	233.45	230.595	1.01238	
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]	219.37	222.086	1.01238	
1760	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [source:swissprot;acc:p05976]	233.45	230.595	1.01238	
1761	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [source:swissprot;acc:p08590]	233.45	230.595	1.01238	
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]	233.45	230.595	1.01238	
1763	myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [source:swissprot;acc:p14649]	233.45	230.595	1.01238	
1764	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	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]	215.698	218.369	1.01238	
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]	228.932	231.732	1.01223	
1767	60s ribosomal protein l24 (l30). [source:swissprot;acc:p38663]	201.288	198.86	1.01221	
1768	estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [source:swissprot;acc:p51659]	185.276	187.534	1.01219	
1769	5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	223.016	225.734	1.01219	
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]	221.082	223.778	1.01219	
1771	putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [source:swissprot;acc:q9uet6]	223.016	225.734	1.01219	
1772	spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [source:swissprot;acc:o15020]	223.032	225.739	1.01214	
1773	spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [source:swissprot;acc:q01082]	223.032	225.739	1.01214	
1774	phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [source:swissprot;acc:o95394]	223.032	225.739	1.01214	

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/