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 2430 to 2479 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
2430	EPN1	epsin 1; eh domain-binding mitotic phosphoprotein. [source:refseq;acc:nm_013333]	217.873	218.644	1.00354	
2431	PSMA2	proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [source:swissprot;acc:p25787]	213.048	212.3	1.00352	
2432	PSMD6	26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [source:swissprot;acc:q15008]	215.807	216.556	1.00347	
2433	EEF1AL3	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [source:swissprot;acc:p04720]	217.366	218.117	1.00346	
2434	MTHFR	methylenetetrahydrofolate reductase (ec 1.5.1.20). [source:swissprot;acc:p42898]	213.021	212.286	1.00346	
2435	ZNF259	zinc-finger protein zpr1 (zinc finger protein 259). [source:swissprot;acc:o75312]	217.366	218.117	1.00346	
2436	EEF1A2	elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [source:swissprot;acc:q05639]	217.366	218.117	1.00346	
2437	GUK1	guanylate kinase (ec 2.7.4.8) (gmp kinase). [source:swissprot;acc:q16774]	219.361	220.116	1.00344	
2438	PSMA4	proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [source:swissprot;acc:p25789]	214.049	213.323	1.0034	
2439	YWHAB	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [source:swissprot;acc:p31946]	220.681	221.425	1.00337	
2440	PSMD3	26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [source:swissprot;acc:o43242]	217.645	218.376	1.00336	
2441	ETFA	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [source:swissprot;acc:p13804]	180.137	180.732	1.0033	
2442	TAF6	transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [source:swissprot;acc:p49848]	204.419	203.748	1.00329	
2443	UBE2I	ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [source:swissprot;acc:p50550]	217.073	216.364	1.00328	
2444	ZBTB20	zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [source:swissprot;acc:q9hc78]	206.086	206.753	1.00324	
2445	ZBTB7B	kruppel-related zinc finger protein hckrox. [source:refseq;acc:nm_015872]	206.088	206.756	1.00324	
2446	EPHX1	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	182.272	181.683	1.00324	
2447	PEX7	peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [source:swissprot;acc:o00628]	206.084	206.752	1.00324	
2448		glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [source:swissprot;acc:p23378]	212.446	211.766	1.00321	
2449	CDS2	phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [source:swissprot;acc:o95674]	204.717	205.371	1.00319	
2450	PSMB6	proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [source:swissprot;acc:p28072]	213.85	213.177	1.00316	
2451	SCAMP2	secretory carrier-associated membrane protein 2. [source:swissprot;acc:o15127]	204.688	205.333	1.00315	
2452	SCAMP3	secretory carrier-associated membrane protein 3. [source:swissprot;acc:o14828]	204.688	205.333	1.00315	
2453	SCAMP1	secretory carrier-associated membrane protein 1. [source:swissprot;acc:o15126]	204.688	205.332	1.00315	
2454	SLC13A4	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [source:swissprot;acc:q9ukg4]	204.683	205.326	1.00314	
2455	SLC13A3	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [source:swissprot;acc:q8wwt9]	204.683	205.326	1.00314	
2456	SLC13A1	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [source:swissprot;acc:q9bzw2]	204.683	205.326	1.00314	
2457	NSF	vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [source:swissprot;acc:p46459]	213.588	212.92	1.00314	
2458	SLC13A2	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [source:swissprot;acc:q13183]	204.683	205.326	1.00314	
2459	CDS1	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	204.653	205.286	1.00309	
2460		pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]	235.812	235.088	1.00308	
2461	SLC20A2	solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [source:refseq;acc:nm_006749]	235.812	235.088	1.00308	
2462	FDPS	farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [source:swissprot;acc:p14324]	235.812	235.088	1.00308	
2463	PCDH15	protocadherin 15 precursor. [source:swissprot;acc:q96qu1]	235.812	235.088	1.00308	
2464	SLC20A1	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [source:refseq;acc:nm_005415]	235.812	235.088	1.00308	
2465	LMBR1L	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	235.812	235.088	1.00308	
2466	GLI1	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [source:swissprot;acc:p08151]	235.812	235.088	1.00308	
2467	SUFU	suppressor of fused. [source:refseq;acc:nm_016169]	235.812	235.088	1.00308	
2468	GLI3	zinc finger protein gli3. [source:swissprot;acc:p10071]	235.812	235.088	1.00308	
2469	LMBR1	limb region 1 protein; limb region 1. [source:refseq;acc:nm_022458]	235.812	235.088	1.00308	
2470	PGC	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [source:swissprot;acc:p20142]	235.812	235.088	1.00308	
2471	GLI2	zinc finger protein gli2 (tax helper protein). [source:swissprot;acc:p10070]	235.812	235.088	1.00308	
2472	TNS3	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [source:refseq;acc:nm_022748]	218.218	217.564	1.00301	
2473	MAPK8IP3	c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [source:swissprot;acc:q9upt6]	218.644	217.991	1.003	
2474	PSMC3	26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [source:swissprot;acc:p17980]	216.64	217.285	1.00298	
2475	TENC1	c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [source:refseq;acc:nm_015319]	218.219	217.571	1.00298	
2476	XYLB	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [source:refseq;acc:nm_005108]	211.205	210.577	1.00298	
2477	MRPL30	mitochondrial ribosomal protein l30 isoform a. [source:refseq;acc:nm_145212]	216.177	216.801	1.00289	
2478	PSMC6	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [source:swissprot;acc:q92524]	216.177	216.801	1.00289	
2479	PRR5	rho-gtpase-activating protein 8. [source:swissprot;acc:q9nsg0]	218.093	218.72	1.00287	

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/