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 3458 to 3507 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1729	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	Divided	187.582	190.028	1.01304	
1730	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [source:swissprot;acc:q8ni60]	Divided	215.336	212.567	1.01303	
1730	p66 alpha. [source:refseq;acc:nm_017660]	Subtracted	167.687	170.455	2.768	
1731	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [source:refseq;acc:nm_052853]	Divided	215.336	212.567	1.01303	
1731	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	Subtracted	167.687	170.455	2.768	
1732	aarf domain containing kinase 4. [source:refseq;acc:nm_024876]	Divided	215.336	212.567	1.01303	
1732	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Subtracted	167.687	170.455	2.768	
1733	6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	Subtracted	240.32	243.085	2.765	
1733	aarf domain containing kinase 1. [source:refseq;acc:nm_020421]	Divided	215.336	212.567	1.01303	
1734	inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [source:swissprot;acc:p29218]	Subtracted	210.366	213.118	2.752	
1734	nucleolar protein family a, member 2; component of the h/aca snornp. [source:refseq;acc:nm_017838]	Divided	221.921	219.081	1.01296	
1735	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	Subtracted	168.018	170.769	2.751	
1735	leucyl-trna synthetase. [source:refseq;acc:nm_020117]	Divided	218.99	216.189	1.01296	
1736	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Subtracted	168.002	170.753	2.751	
1736	transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [source:swissprot;acc:p35269]	Divided	221.921	219.081	1.01296	
1737	6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	Subtracted	240.32	243.069	2.749	
1737	probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [source:swissprot;acc:q15031]	Divided	218.99	216.189	1.01296	
1738	g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	Subtracted	168.098	170.844	2.746	
1738	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [source:swissprot;acc:q9y234]	Divided	206.595	209.258	1.01289	
1739	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	Subtracted	168.091	170.837	2.746	
1739	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [source:swissprot;acc:p23258]	Divided	206.595	209.258	1.01289	
1740	defender against cell death 1 (dad-1). [source:swissprot;acc:p46966]	Divided	206.595	209.258	1.01289	
1740	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]	Subtracted	210.358	213.103	2.745	
1741	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [source:swissprot;acc:p06493]	Subtracted	168.145	170.888	2.743	
1741	t-complex 11. [source:refseq;acc:nm_018679]	Divided	206.595	209.258	1.01289	
1742	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [source:swissprot;acc:q9uj68]	Subtracted	220.091	217.362	2.729	
1742	tubulin gamma-2 chain (gamma-2 tubulin). [source:swissprot;acc:q9nrh3]	Divided	206.595	209.258	1.01289	
1743	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [source:swissprot;acc:q9y617]	Subtracted	220.091	217.362	2.729	
1743	pre-mrna cleavage factor i, 59 kda subunit. [source:refseq;acc:nm_024811]	Divided	218.176	215.402	1.01288	
1744	megf6 (fragment). [source:sptrembl;acc:o75095]	Subtracted	221.811	219.09	2.721	
1744	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [source:refseq;acc:nm_003901]	Divided	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]	Divided	219.423	222.215	1.01272	
1745	brca1-associated ring domain protein 1 (bard-1). [source:swissprot;acc:q99728]	Subtracted	216.271	218.991	2.72	
1746	5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	Subtracted	223.016	225.734	2.718	
1746	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [source:swissprot;acc:p04181]	Divided	219.423	222.215	1.01272	
1747	putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [source:swissprot;acc:q9uet6]	Subtracted	223.016	225.734	2.718	
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]	Divided	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]	Divided	215.673	212.971	1.01269	
1748	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]	Subtracted	219.37	222.086	2.716	
1749	dna mismatch repair protein mlh3 (mutl protein homolog 3). [source:swissprot;acc:q9uhc1]	Divided	206.058	203.485	1.01264	
1749	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	Subtracted	206.823	204.111	2.712	
1750	similar to lim domain only 7 (fragment). [source:sptrembl;acc:q8n6m2]	Divided	216.27	213.57	1.01264	
1750	spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [source:swissprot;acc:o15020]	Subtracted	223.032	225.739	2.707	
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]	Divided	221.185	223.97	1.01259	
1751	spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [source:swissprot;acc:q01082]	Subtracted	223.032	225.739	2.707	
1752	brca1-associated ring domain protein 1 (bard-1). [source:swissprot;acc:q99728]	Divided	216.271	218.991	1.01258	
1752	phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [source:swissprot;acc:o95394]	Subtracted	223.032	225.739	2.707	
1753	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	Subtracted	206.549	203.844	2.705	
1753	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [source:swissprot;acc:q9uj68]	Divided	220.091	217.362	1.01256	
1754	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	Subtracted	206.549	203.844	2.705	

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/