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 2080 to 2129 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison	
2080	PIK3C2B	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	215.967	214.28	1.00787	
2081	DNM1L	dynamin 1-like protein isoform 3; dynamin-like protein. [source:refseq;acc:nm_005690]	215.967	214.28	1.00787	
2082	PIK3C2A	phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [source:refseq;acc:nm_002645]	215.967	214.28	1.00787	
2083	PTPRA	vacuolar protein sorting 16 (hvps16). [source:swissprot;acc:q9h269]	215.258	213.579	1.00786	
2084		glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [source:swissprot;acc:q06210]	222.548	224.293	1.00784	
2085	IDH3A	isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:p50213]	222.58	224.32	1.00782	
2086	IDH3B	isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:o43837]	222.58	224.32	1.00782	
2087	IDH3G	isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:p51553]	222.58	224.32	1.00782	
2088	MPP3	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [source:swissprot;acc:q13368]	218.124	216.433	1.00781	
2089	UTP14A	serologically defined colon cancer antigen 16. [source:refseq;acc:nm_006649]	215.144	213.479	1.0078	
2090	GFPT2	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [source:swissprot;acc:o94808]	222.609	224.344	1.00779	
2091	SNUPN	rna, u transporter 1; snurportin-1. [source:refseq;acc:nm_005701]	211.679	210.052	1.00775	
2092	ECSIT	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [source:refseq;acc:nm_016581]	211.992	210.369	1.00772	
2093	RBKS	ribokinase (ec 2.7.1.15). [source:swissprot;acc:q9h477]	209.994	208.387	1.00771	
2094	PMS2	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	207.321	205.747	1.00765	
2095	POLS	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [source:refseq;acc:nm_006999]	229.266	227.53	1.00763	
2096	CCDC92	limkain beta 2. [source:refseq;acc:nm_025140]	217.723	216.089	1.00756	
2097	CCDC85B	delta-interacting protein a (hepatitis delta antigen interacting protein a). [source:swissprot;acc:q15834]	214.979	213.39	1.00745	
2098		ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	177.515	178.831	1.00741	
2099	SUMO3	ubiquitin-like protein smt3a. [source:swissprot;acc:p55854]	211.71	213.27	1.00737	
2100		ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	211.71	213.27	1.00737	
2101	ACRC	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	211.71	213.27	1.00737	
2102	EIF5AP1	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [source:swissprot;acc:p10159]	208.727	210.263	1.00736	
2103	TKT	transketolase (ec 2.2.1.1) (tk). [source:swissprot;acc:p29401]	214.666	216.236	1.00731	
2104	DTYMK	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [source:swissprot;acc:p23919]	209.328	207.813	1.00729	
2105	EIF5A2	eif-5a2 protein. [source:refseq;acc:nm_020390]	208.591	210.111	1.00729	
2106	ISL1	insulin gene enhancer protein isl-1 (islet-1). [source:swissprot;acc:p20663]	197.489	196.061	1.00728	
2107	LMO7	lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [source:refseq;acc:nm_005358]	216.23	217.801	1.00727	
2108	ASL	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	216.36	217.93	1.00726	
2109	RANBP2	ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [source:swissprot;acc:p49792]	219.032	217.47	1.00718	
2110	COG6	conserved oligomeric golgi complex component 6. [source:swissprot;acc:q9y2v7]	211.099	209.607	1.00712	
2111		ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	219.047	217.511	1.00706	
2112	POLR3K	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [source:swissprot;acc:q9y2y1]	223.415	224.989	1.00705	
2113		ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	219.055	217.533	1.007	
2114	LIPF	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [source:swissprot;acc:p07098]	214.632	213.14	1.007	
2115	LIPM	ba304i5.1 (novel lipase) (fragment). [source:sptrembl;acc:q96lg2]	214.632	213.14	1.007	
2116	LIPA	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [source:swissprot;acc:p38571]	214.632	213.14	1.007	
2117	SARS2	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [source:swissprot;acc:q9np81]	214.632	213.14	1.007	
2118	SARS	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [source:swissprot;acc:p49591]	214.632	213.14	1.007	
2119	KCMF1	potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [source:refseq;acc:nm_020122]	221.248	222.788	1.00696	
2120	SLC23A1	solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [source:swissprot;acc:q9uhi7]	221.248	222.788	1.00696	
2121	HNRPA3	heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [source:swissprot;acc:p51991]	221.248	222.788	1.00696	
2122	LGALS9	galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	206.473	207.911	1.00696	
2123	ARF4	adp-ribosylation factor 4. [source:swissprot;acc:p18085]	221.248	222.788	1.00696	
2124	AKTIP	fused toes homolog; likely ortholog of mouse fused toes. [source:refseq;acc:nm_022476]	221.248	222.788	1.00696	
2125	SHC1	shc transforming protein. [source:swissprot;acc:p29353]	221.248	222.788	1.00696	
2126	ZNF289	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [source:refseq;acc:nm_032389]	221.248	222.788	1.00696	
2127	SHC3	neuronal shc. [source:refseq;acc:nm_016848]	221.248	222.788	1.00696	
2128	ARF1	adp-ribosylation factor 1. [source:swissprot;acc:p32889]	221.248	222.788	1.00696	
2129	HNRNPA1	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [source:swissprot;acc:p09651]	221.248	222.788	1.00696	

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/