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

Results: HTML CSV LaTeX

Showing element 1701 to 1750 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison	
1701	G6PD	glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [source:swissprot;acc:p11413]	216.079	219.024	1.01363	
1702	XRCC3	dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [source:swissprot;acc:o43542]	216.079	219.024	1.01363	
1703	RECQL5	atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [source:swissprot;acc:o94762]	216.079	219.024	1.01363	
1704		ataxin 2-binding protein. [source:swissprot;acc:q9nwb1]	218.514	215.577	1.01362	
1705	PPP4C	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [source:swissprot;acc:p33172]	223.846	220.847	1.01358	
1706	IGBP1	immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [source:swissprot;acc:p78318]	223.846	220.847	1.01358	
1707	BUB1B	mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [source:swissprot;acc:o60566]	221.283	218.334	1.01351	
1708	PNPO	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	221.283	218.334	1.01351	
1709	HHEX	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [source:swissprot;acc:q03014]	198.014	195.385	1.01346	
1710		casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [source:swissprot;acc:p49674]	227.225	224.21	1.01345	
1711	HLCS	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [source:swissprot;acc:p50747]	218.436	215.553	1.01337	
1712	TAF11	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	SH3GL3	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	206.823	204.111	1.01329	
1714	ARMET	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	206.549	203.844	1.01327	
1715	HDC	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	206.549	203.844	1.01327	
1716	SH3GL2	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	OSGEP	o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	221.058	218.164	1.01327	
1718	SH3GL1	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	DDX12	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	CSNK1D	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [source:swissprot;acc:p48730]	227.125	224.164	1.01321	
1722	RPS13	40s ribosomal protein s13. [source:swissprot;acc:q02546]	220.899	223.813	1.01319	
1723	NADK	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	IPMK	inositol polyphosphate multikinase. [source:refseq;acc:nm_152230]	217.676	220.53	1.01311	
1725	AFG3L2	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [source:swissprot;acc:q9y4w6]	217.676	220.53	1.01311	
1726	FUT8	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	IMPA1	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	IMPA2	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	ATG12	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	187.582	190.028	1.01304	
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	

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/