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 1313 to 1362 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
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	
1351	PHB	prohibitin. [source:swissprot;acc:p35232]	211.513	206.941	1.02209	
1352		repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	211.513	206.941	1.02209	
1353	NDST2	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [source:swissprot;acc:p52849]	228.409	223.475	1.02208	
1354	NDST3	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [source:refseq;acc:nm_004784]	228.409	223.475	1.02208	
1355	NDST4	n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569]	228.409	223.475	1.02208	
1356	NDST1	heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [source:swissprot;acc:p52848]	228.409	223.475	1.02208	
1357	CDC27	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260]	228.409	223.475	1.02208	
1358	USF1	upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415]	214.987	210.359	1.022	
1359	GSTT2B	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	228.642	223.726	1.02197	
1360	TGFBR1	tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [source:swissprot;acc:p36897]	223.89	228.805	1.02195	
1361	USF2	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [source:swissprot;acc:q15853]	214.971	210.354	1.02195	
1362	PAOX	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	228.644	223.736	1.02194	

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/