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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1730 to 1779 of 3228 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
1730	CABC1	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [source:swissprot;acc:q8ni60]	215.336	212.567	1.01303	
1731	ADCK2	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [source:refseq;acc:nm_052853]	215.336	212.567	1.01303	
1732	ADCK4	aarf domain containing kinase 4. [source:refseq;acc:nm_024876]	215.336	212.567	1.01303	
1733	ADCK1	aarf domain containing kinase 1. [source:refseq;acc:nm_020421]	215.336	212.567	1.01303	
1734	NOLA2	nucleolar protein family a, member 2; component of the h/aca snornp. [source:refseq;acc:nm_017838]	221.921	219.081	1.01296	
1735	LARS	leucyl-trna synthetase. [source:refseq;acc:nm_020117]	218.99	216.189	1.01296	
1736	GTF2F1	transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [source:swissprot;acc:p35269]	221.921	219.081	1.01296	
1737	LARS2	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	LIPT1	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [source:swissprot;acc:q9y234]	206.595	209.258	1.01289	
1739	TUBG1	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	DAD1	defender against cell death 1 (dad-1). [source:swissprot;acc:p46966]	206.595	209.258	1.01289	
1741	TCP11	t-complex 11. [source:refseq;acc:nm_018679]	206.595	209.258	1.01289	
1742	TUBG2	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	SGPL1	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	OAT	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [source:swissprot;acc:p04181]	219.423	222.215	1.01272	
1747	ERCC2	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	MLH3	dna mismatch repair protein mlh3 (mutl protein homolog 3). [source:swissprot;acc:q9uhc1]	206.058	203.485	1.01264	
1750	LIMCH1	similar to lim domain only 7 (fragment). [source:sptrembl;acc:q8n6m2]	216.27	213.57	1.01264	
1751	AP1M2	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	BARD1	brca1-associated ring domain protein 1 (bard-1). [source:swissprot;acc:q99728]	216.271	218.991	1.01258	
1753	MSRA	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	PSAT1	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [source:swissprot;acc:q9y617]	220.091	217.362	1.01256	
1755	CTPS	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	180.609	178.393	1.01242	
1756	MEGF6	megf6 (fragment). [source:sptrembl;acc:o75095]	221.811	219.09	1.01242	
1757	CTPS2	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	PCYT2	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	233.45	230.595	1.01238	
1759	RUVBL1	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	MYL1	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [source:swissprot;acc:p05976]	233.45	230.595	1.01238	
1761	MYL3	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [source:swissprot;acc:p08590]	233.45	230.595	1.01238	
1762	NDUFS6	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	MYL6	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	MTHFD1	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	RPL24	60s ribosomal protein l24 (l30). [source:swissprot;acc:p38663]	201.288	198.86	1.01221	
1768	HSD17B4	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	MTAP	5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	223.016	225.734	1.01219	
1770	AP1M1	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	FTSJ1	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	SPTBN2	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	SPTBN1	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	PGM3	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	
1775	SPTLC1	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]	207.757	210.274	1.01212	
1776	NUPL1	nucleoporin like 1. [source:refseq;acc:nm_014089]	216.878	214.286	1.0121	
1777	ARHGEF4	rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [source:refseq;acc:nm_015320]	216.878	214.286	1.0121	
1778	ARHGEF9	cdc42 guanine exchange factor 9; hpem-2 collybistin. [source:refseq;acc:nm_015185]	216.878	214.286	1.0121	
1779	PBX1	pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [source:swissprot;acc:p40424]	206.332	203.874	1.01206	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/