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 1301 to 1350 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
1301	TPD52L2	tumor protein d54 (hd54) (d52-like 2). [source:swissprot;acc:o43399]	206.852	211.757	1.02371	
1302	UQCRC1	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [source:swissprot;acc:p31930]	217.624	212.584	1.02371	
1303	FHL5	activator of camp-responsive element modulator (crem) in testis; lim protein act. [source:refseq;acc:nm_020482]	269.157	275.531	1.02368	
1304	GSR	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [source:swissprot;acc:p00390]	207.387	212.275	1.02357	
1305	PPP3CA	serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [source:swissprot;acc:q08209]	218.439	213.436	1.02344	
1306	PPP3CC	serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [source:swissprot;acc:p48454]	218.441	213.441	1.02343	
1307	PPP3CB	serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [source:swissprot;acc:p16299]	218.44	213.44	1.02343	
1308	OCA2	p protein (melanocyte-specific transporter protein). [source:swissprot;acc:q04671]	218.44	213.439	1.02343	
1309	VBP1	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	226.439	221.26	1.02341	
1310	PFDN2	prefoldin subunit 2 (hspc231). [source:swissprot;acc:q9uhv9]	226.439	221.26	1.02341	
1311	UXT	uxt protein (ubiquitously expressed transcript protein) (hspc024). [source:swissprot;acc:q9ubk9]	226.439	221.26	1.02341	
1312	RAD50	rad50 homolog isoform 1. [source:refseq;acc:nm_005732]	199.739	204.407	1.02337	
1313	STAT3	signal transducer and activator of transcription 3 (acute-phase response factor). [source:swissprot;acc:p40763]	222.573	227.75	1.02326	
1314	STAT4	signal transducer and activator of transcription 4. [source:swissprot;acc:q14765]	222.573	227.751	1.02326	
1315	STAT1	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [source:swissprot;acc:p42224]	222.574	227.752	1.02326	
1316	STAT6	signal transducer and activator of transcription 6 (il-4 stat). [source:swissprot;acc:p42226]	222.569	227.739	1.02323	
1317	CENPJ	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	206.773	202.105	1.0231	
1318	STAT5A	signal transducer and activator of transcription 5a. [source:swissprot;acc:p42229]	222.546	227.673	1.02304	
1319	GYS1	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	159.75	156.153	1.02304	
1320	STAT5B	signal transducer and activator of transcription 5b. [source:swissprot;acc:p51692]	222.544	227.667	1.02302	
1321	DIMT1L	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [source:swissprot;acc:q9unq2]	226.347	221.259	1.023	
1322		endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	159.86	156.275	1.02294	
1323	NCK2	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	205.225	200.625	1.02293	
1324	GYS2	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	159.993	156.421	1.02284	
1325	WRNIP1	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	217.133	212.289	1.02282	
1326	CSMD1	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	218.509	213.648	1.02275	
1327	ZIC4	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [source:swissprot;acc:q8n9l1]	218.509	213.648	1.02275	
1328	RCAN2	calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [source:swissprot;acc:q14206]	218.509	213.649	1.02275	
1329		dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	218.509	213.648	1.02275	
1330	RCAN1	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [source:swissprot;acc:p53805]	218.508	213.648	1.02275	
1331	RCAN3	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [source:swissprot;acc:q9uka8]	218.509	213.649	1.02275	
1332	OXA1L	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [source:swissprot;acc:q15070]	220.681	215.78	1.02271	
1333	MRPL34	60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48]	220.681	215.78	1.02271	
1334	PRAF2	jm4 protein. [source:refseq;acc:nm_007213]	199.643	204.163	1.02264	
1335	ARL6IP5	cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [source:refseq;acc:nm_006407]	199.771	204.287	1.02261	
1336	GALK2	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	215.162	210.412	1.02257	
1337		galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	215.162	210.412	1.02257	
1338	GALE	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	215.162	210.412	1.02257	
1339	NPC2	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [source:swissprot;acc:q15668]	205.204	200.71	1.02239	
1340	SUV39H2	histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [source:swissprot;acc:q9h5i1]	226.433	231.491	1.02234	
1341	EIF2S1	eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [source:swissprot;acc:p05198]	226.433	231.491	1.02234	
1342	SUV39H1	histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [source:swissprot;acc:o43463]	226.433	231.491	1.02234	
1343	CDC25A	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [source:swissprot;acc:p30304]	258.558	252.916	1.02231	
1344	EXO1	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [source:refseq;acc:nm_006027]	216.772	221.594	1.02224	
1345	FANCL	phd finger protein 9. [source:refseq;acc:nm_018062]	216.772	221.594	1.02224	
1346	SOLH	small optic lobes homolog; small optic lobes, drosophila, homolog of. [source:refseq;acc:nm_005632]	216.772	221.594	1.02224	
1347	LIAS	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [source:swissprot;acc:o43766]	204.961	209.517	1.02223	
1348	ZIC1	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915]	218.569	213.832	1.02215	
1349	ZIC3	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481]	218.572	213.841	1.02212	
1350	ZIC2	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [source:swissprot;acc:o95409]	218.574	213.847	1.0221	

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/