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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1712 to 1761 of 3228 in total

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

Rank	description	red	green	network_comparison	
1712	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [source:swissprot;acc:q15544]	208.598	211.375	1.01331	
1713	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	206.823	204.111	1.01329	
1714	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	206.549	203.844	1.01327	
1715	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	206.549	203.844	1.01327	
1716	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [source:swissprot;acc:q99962]	206.522	203.818	1.01327	
1717	o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	221.058	218.164	1.01327	
1718	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]	206.251	203.553	1.01325	
1719	helicase (fragment). [source:sptrembl;acc:q92771]	187.204	189.679	1.01322	
1720	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	187.205	189.679	1.01322	
1721	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [source:swissprot;acc:p48730]	227.125	224.164	1.01321	
1722	40s ribosomal protein s13. [source:swissprot;acc:q02546]	220.899	223.813	1.01319	
1723	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [source:swissprot;acc:o95544]	212.36	215.147	1.01312	
1724	inositol polyphosphate multikinase. [source:refseq;acc:nm_152230]	217.676	220.53	1.01311	
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	

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/