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 1177 to 1226 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison	
1177	ACBD3	golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [source:refseq;acc:nm_022735]	218.186	212.672	1.02593	
1178	SGCD	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q92629]	218.186	212.672	1.02593	
1179	MARCH8	cellular modulator of immune recognition. [source:refseq;acc:nm_145021]	218.186	212.672	1.02593	
1180	ATP6V0B	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [source:swissprot;acc:q99437]	218.186	212.672	1.02593	
1181	SGCG	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q13326]	218.186	212.672	1.02593	
1182	NCALD	neurocalcin delta. [source:swissprot;acc:p29554]	225.104	230.931	1.02589	
1183	HPCA	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [source:swissprot;acc:p32076]	225.103	230.928	1.02588	
1184	GIT1	arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [source:swissprot;acc:q9y2x7]	216.729	222.334	1.02586	
1185	HPCAL1	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [source:swissprot;acc:p37235]	225.094	230.913	1.02585	
1186		adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [source:swissprot;acc:p56559]	218.402	212.904	1.02582	
1187	ATP6V0D1	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [source:swissprot;acc:p12953]	218.402	212.904	1.02582	
1188	ARL4A	adp-ribosylation factor-like protein 4. [source:swissprot;acc:p40617]	218.402	212.904	1.02582	
1189		alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [source:swissprot;acc:p19652]	209.649	204.406	1.02565	
1190	UBB	ubiquitin. [source:swissprot;acc:p02248]	209.6	204.372	1.02558	
1191	UBP1	upstream binding protein 1 (lbp-1a). [source:refseq;acc:nm_014517]	220.742	215.237	1.02558	
1192	TFCP2	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	220.742	215.237	1.02558	
1193	TFCP2L1	lbp-9. [source:refseq;acc:nm_014553]	220.742	215.237	1.02558	
1194	SFRS3	splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [source:swissprot;acc:p23152]	220.742	215.237	1.02558	
1195	FHL2	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [source:swissprot;acc:q14192]	269.608	276.493	1.02554	
1196	KIF2B	kinesin protein. [source:refseq;acc:nm_032559]	224.858	219.264	1.02551	
1197	KCTD10	mstp028 protein. [source:refseq;acc:nm_031954]	219.042	213.6	1.02548	
1198	FHL3	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [source:swissprot;acc:q13643]	269.59	276.454	1.02546	
1199	MPHOSPH10	u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [source:swissprot;acc:o00566]	241.496	235.508	1.02543	
1200	SMARCB1	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [source:swissprot;acc:q12824]	219.03	213.604	1.0254	
1201	SDHA	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [source:swissprot;acc:p31040]	210.986	216.344	1.0254	
1202	DPH2	diphthamide biosynthesis-like protein 2. [source:refseq;acc:nm_001384]	227.274	233.041	1.02537	
1203	TNFAIP1	tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [source:swissprot;acc:q13829]	219.023	213.606	1.02536	
1204	KCTD13	polymerase delta-interacting protein 1; tnfaip1-like. [source:refseq;acc:nm_178863]	219.022	213.607	1.02535	
1205	KIF21A	ny-ren-62 antigen (fragment). [source:sptrembl;acc:q9y590]	224.805	219.251	1.02533	
1206		integral membrane protein cii-3b. [source:sptrembl;acc:o75609]	207.646	212.891	1.02526	
1207	SDHC	succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [source:swissprot;acc:q99643]	207.644	212.888	1.02525	
1208		signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	224.878	219.342	1.02524	
1209	SDHB	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [source:swissprot;acc:p21912]	207.931	213.175	1.02522	
1210	KIF2A	kinesin-like protein kif2 (kinesin-2) (hk2). [source:swissprot;acc:o00139]	224.764	219.241	1.02519	
1211	C11orf2	chromosome 11 open reading frame2; chromosome  11 open reading frame2. [source:refseq;acc:nm_013265]	214.364	219.759	1.02517	
1212	KIF13A	kinesin-like protein kif13a (kinesin-like protein rbkin). [source:swissprot;acc:q9h1h9]	214.364	219.759	1.02517	
1213	COG2	conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [source:swissprot;acc:q14746]	214.364	219.759	1.02517	
1214		kinesin-like protein kif13b (kinesin-like protein gakin). [source:swissprot;acc:q9nqt8]	214.364	219.759	1.02517	
1215	DAZAP1	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	218.268	212.916	1.02514	
1216	ZMIZ1	retinoic acid induced 17; pias-like protein hzimp10. [source:refseq;acc:nm_020338]	218.269	212.918	1.02513	
1217	QRSL1	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [source:refseq;acc:nm_018292]	211.959	217.258	1.025	
1218	FAAH	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [source:swissprot;acc:o00519]	211.959	217.258	1.025	
1219	COTL1	coactosin-like protein. [source:swissprot;acc:q14019]	211.959	217.258	1.025	
1220	UNG	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [source:swissprot;acc:p13051]	211.959	217.258	1.025	
1221	PET112L	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [source:swissprot;acc:o75879]	211.959	217.258	1.025	
1222	TPD52L1	tumor protein d53 (hd53) (d52-like 1). [source:swissprot;acc:q16890]	206.774	211.936	1.02496	
1223	TPD52	tumor protein d52 (n8 protein). [source:swissprot;acc:p55327]	206.771	211.926	1.02493	
1224	FPGS	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [source:swissprot;acc:q05932]	225.906	231.524	1.02487	
1225	UBE2E1	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [source:swissprot;acc:p51965]	166.846	170.989	1.02483	
1226	UBE2E4P	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [source:refseq;acc:nm_006357]	166.846	170.989	1.02483	

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/