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 1008 to 1057 of 3228 in total

Value Type

: Ranked
Network Comparison Type

: Divided
Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	description	red	green	network_comparison
1008	WDR46	wd-repeat protein bing4. [swissprot;acc:o15213]	243.227	235.475	1.03292
1009	no value	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	229.116	221.823	1.03288
1010	CROT	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	217.523	210.648	1.03264
1011	RBL2	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	217.026	210.189	1.03253
1012	RBL1	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	217.021	210.185	1.03252
1013	HEATR1	protein bap28. [swissprot;acc:q9h583]	244.312	236.647	1.03239
1014	AATF	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	243.045	235.422	1.03238
1015	MAGI1	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	221.73	228.906	1.03236
1016	KPNA4	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	217.369	210.561	1.03233
1017	TOE1	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	217.365	210.558
1018	KPNA3	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	217.361	210.554
1019	TYRL	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	221.302	214.409	1.03215
1020	DCT	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	221.28		1.03205
1021	TYRP1	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	221.278		1.03204
1022	CBS	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	205.632	199.266	1.03195
1023	RHOC	transforming protein rhoc (h9). [swissprot;acc:p08134]
1024	TST	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
1025	MPST	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
1026	RHOA	transforming protein rhoa (h12). [swissprot;acc:p06749]
1027	SUCLG1	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597]	211.908	218.627	1.03171
1028	SUCLA2	succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7]	211.908	218.627	1.03171
1029	DDB1	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]	222.364	215.535	1.03168
1030	PCCB	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166]	222.364	215.535	1.03168
1031	EMG1	probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	242.978	235.518	1.03167
1032	AGPAT2	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]	186.664	180.943	1.03162
1033	TYR	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679]	221.183	214.406	1.03161
1034	ESRRB	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	186.551	180.837	1.0316
1035	MAGI2	atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]	221.682	228.68	1.03157
1036	COPB1	coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618]	171.341	176.746	1.03155
1037	GLRX3	thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541]	228.412	235.609	1.03151
1038	no value	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]	186.741	181.041	1.03148
1039	DLD	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622]	207.719	214.236	1.03137
1040	CCT5	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643]	163.24	168.359	1.03136
1041	HNRNPL	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	186.774	181.099	1.03134
1042	no value	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	186.799	181.127	1.03132
1043	AGPAT3	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7]	187.834	182.137	1.03128
1044	DYNLT3	t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808]	173.475	178.889	1.03121
1045	FIP1L1	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	115.817	119.432
1046	MRE11A	double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]	173.475	178.889
1047	ESRRA	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	187.022	181.391	1.03104
1048	AGPAT4	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5]	187.96	182.308	1.031
1049	no value	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	211.449	217.998	1.03097
1050	HSD17B1	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]
1051	no value	17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
1052	RDH8	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725]
1053	PSMA5	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066]	207.04	200.84	1.03087
1054	no value	60s ribosomal protein l21. [swissprot;acc:p46778]	223.958	217.263	1.03082
1055	ASNSD1	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	219.01	212.468	1.03079
1056	ATP6V1A	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]
1057	ASNS	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/