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 2601 to 2650 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
1301	COPE	coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [source:swissprot;acc:o14579]	Subtracted	187.964	192.849	4.885	
1301	TPD52L2	tumor protein d54 (hd54) (d52-like 2). [source:swissprot;acc:o43399]	Divided	206.852	211.757	1.02371	
1302	CSMD1	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	Subtracted	218.509	213.648	4.861	
1302	UQCRC1	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [source:swissprot;acc:p31930]	Divided	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]	Divided	269.157	275.531	1.02368	
1303	ZIC4	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [source:swissprot;acc:q8n9l1]	Subtracted	218.509	213.648	4.861	
1304		dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	Subtracted	218.509	213.648	4.861	
1304	GSR	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [source:swissprot;acc:p00390]	Divided	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]	Divided	218.439	213.436	1.02344	
1305	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]	Subtracted	218.509	213.649	4.86	
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]	Divided	218.441	213.441	1.02343	
1306	RCAN1	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [source:swissprot;acc:p53805]	Subtracted	218.508	213.648	4.86	
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]	Divided	218.44	213.44	1.02343	
1307	RCAN3	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [source:swissprot;acc:q9uka8]	Subtracted	218.509	213.649	4.86	
1308	OCA2	p protein (melanocyte-specific transporter protein). [source:swissprot;acc:q04671]	Divided	218.44	213.439	1.02343	
1308	WRNIP1	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Subtracted	217.133	212.289	4.844	
1309	EXO1	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [source:refseq;acc:nm_006027]	Subtracted	216.772	221.594	4.822	
1309	VBP1	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	Divided	226.439	221.26	1.02341	
1310	FANCL	phd finger protein 9. [source:refseq;acc:nm_018062]	Subtracted	216.772	221.594	4.822	
1310	PFDN2	prefoldin subunit 2 (hspc231). [source:swissprot;acc:q9uhv9]	Divided	226.439	221.26	1.02341	
1311	SOLH	small optic lobes homolog; small optic lobes, drosophila, homolog of. [source:refseq;acc:nm_005632]	Subtracted	216.772	221.594	4.822	
1311	UXT	uxt protein (ubiquitously expressed transcript protein) (hspc024). [source:swissprot;acc:q9ubk9]	Divided	226.439	221.26	1.02341	
1312	GALK2	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	Subtracted	215.162	210.412	4.75	
1312	RAD50	rad50 homolog isoform 1. [source:refseq;acc:nm_005732]	Divided	199.739	204.407	1.02337	
1313		galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	Subtracted	215.162	210.412	4.75	
1313	STAT3	signal transducer and activator of transcription 3 (acute-phase response factor). [source:swissprot;acc:p40763]	Divided	222.573	227.75	1.02326	
1314	GALE	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	Subtracted	215.162	210.412	4.75	
1314	STAT4	signal transducer and activator of transcription 4. [source:swissprot;acc:q14765]	Divided	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]	Divided	222.574	227.752	1.02326	
1315	ZIC1	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915]	Subtracted	218.569	213.832	4.737	
1316	STAT6	signal transducer and activator of transcription 6 (il-4 stat). [source:swissprot;acc:p42226]	Divided	222.569	227.739	1.02323	
1316	ZIC3	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481]	Subtracted	218.572	213.841	4.731	
1317	CENPJ	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	Divided	206.773	202.105	1.0231	
1317	ZIC2	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [source:swissprot;acc:o95409]	Subtracted	218.574	213.847	4.727	
1318	CREB5	camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904]	Subtracted	218.591	213.899	4.692	
1318	STAT5A	signal transducer and activator of transcription 5a. [source:swissprot;acc:p42229]	Divided	222.546	227.673	1.02304	
1319	CENPJ	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	Subtracted	206.773	202.105	4.668	
1319	GYS1	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	Divided	159.75	156.153	1.02304	
1320	RAD50	rad50 homolog isoform 1. [source:refseq;acc:nm_005732]	Subtracted	199.739	204.407	4.668	
1320	STAT5B	signal transducer and activator of transcription 5b. [source:swissprot;acc:p51692]	Divided	222.544	227.667	1.02302	
1321	CDC25C	m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [source:swissprot;acc:p30307]	Subtracted	259.439	254.797	4.642	
1321	DIMT1L	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [source:swissprot;acc:q9unq2]	Divided	226.347	221.259	1.023	
1322		endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	Divided	159.86	156.275	1.02294	
1322	SOCS1	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [source:swissprot;acc:o15524]	Subtracted	216.542	211.908	4.634	
1323	GMFG	glia maturation factor gamma (gmf-gamma). [source:swissprot;acc:o60234]	Subtracted	216.542	211.908	4.634	
1323	NCK2	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	Divided	205.225	200.625	1.02293	
1324	ASCC2	asc-1 complex subunit p100. [source:refseq;acc:nm_032204]	Subtracted	216.542	211.908	4.634	
1324	GYS2	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	Divided	159.993	156.421	1.02284	
1325	FKBP1A	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [source:swissprot;acc:p20071]	Subtracted	216.542	211.908	4.634	
1325	WRNIP1	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Divided	217.133	212.289	1.02282	

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/