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 1430 to 1479 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
1430	DUT	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	187.114	190.925	1.02037	
1431	RAD23A	uv excision repair protein rad23 homolog a (hhr23a). [source:swissprot;acc:p54725]	220.987	225.468	1.02028	
1432	PSMD4	26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [source:swissprot;acc:p55036]	220.987	225.468	1.02028	
1433	OCRL	inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [source:swissprot;acc:q01968]	220.987	225.468	1.02028	
1434	RAD23B	uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [source:swissprot;acc:p54727]	220.987	225.468	1.02028	
1435		myosin vi. [source:swissprot;acc:q9um54]	220.987	225.468	1.02028	
1436	EVI5L	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_145245]	218.829	214.493	1.02022	
1437	EVI5	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_005665]	218.829	214.493	1.02022	
1438	PGGT1B	geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [source:swissprot;acc:p53609]	225.039	229.573	1.02015	
1439	FADS3	fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [source:refseq;acc:nm_021727]	225.039	229.573	1.02015	
1440	SMAD4	mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [source:swissprot;acc:q13485]	225.039	229.573	1.02015	
1441	FADS2	fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [source:refseq;acc:nm_004265]	225.039	229.573	1.02015	
1442		fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402]	225.039	229.573	1.02015	
1443	GLUD2	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [source:swissprot;acc:p49448]	203.908	207.998	1.02006	
1444	GLUDP5	glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [source:swissprot;acc:p00367]	203.908	207.998	1.02006	
1445	PCF11	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	134.233	136.922	1.02003	
1446	HSPB1	heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [source:swissprot;acc:p04792]	221.817	226.23	1.01989	
1447	POLE3	dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [source:swissprot;acc:q9nrf9]	250.854	255.842	1.01988	
1448	ZMPSTE24	caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [source:swissprot;acc:o75844]	226.532	222.117	1.01988	
1449	TNPO3	transportin-sr; importin 12. [source:refseq;acc:nm_012470]	225.305	229.766	1.0198	
1450	HSPB8	alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [source:swissprot;acc:q9ujy1]	221.804	226.194	1.01979	
1451	BOLA2B	my016 protein. [source:sptrembl;acc:q9h3k6]	224.755	229.2	1.01978	
1452		cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	160.381	163.554	1.01978	
1453	RTN4	reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [source:swissprot;acc:q9nqc3]	207.038	211.13	1.01976	
1454	SAP18	sin3 associated polypeptide p18 (2hor0202). [source:swissprot;acc:o00422]	207.024	211.089	1.01964	
1455	EHD1	eh-domain containing protein 1 (testilin) (hpast1). [source:swissprot;acc:q9h4m9]	207.024	211.085	1.01962	
1456	EHD4	eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [source:swissprot;acc:q9h223]	207.024	211.086	1.01962	
1457	EHD2	eh-domain containing protein 2. [source:swissprot;acc:q9nzn4]	207.024	211.086	1.01962	
1458	EHD3	eh-domain containing protein 3. [source:swissprot;acc:q9nzn3]	207.024	211.086	1.01962	
1459	CSE1L	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [source:swissprot;acc:p55060]	192.336	188.637	1.01961	
1460	TRIP12	thyroid receptor interacting protein 12 (trip12). [source:swissprot;acc:q14669]	205.817	209.851	1.0196	
1461	RTN1	reticulon 1 (neuroendocrine-specific protein). [source:swissprot;acc:q16799]	207.019	211.077	1.0196	
1462	DLSTP	dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [source:swissprot;acc:p36957]	205.817	209.851	1.0196	
1463		pnas-18. [source:sptrembl;acc:q9bzu3]	161.056	164.211	1.01959	
1464		poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	217.351	213.18	1.01957	
1465	MTO1	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	217.351	213.18	1.01957	
1466	RTN2	reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [source:swissprot;acc:o75298]	207.022	211.073	1.01957	
1467	MPP2	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [source:swissprot;acc:q14168]	228.513	232.983	1.01956	
1468	DRAP1	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [source:refseq;acc:nm_006442]	212.001	207.937	1.01954	
1469	RTN3	reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [source:swissprot;acc:o95197]	207.013	211.05	1.0195	
1470	QARS	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [source:swissprot;acc:p47897]	221.412	217.199	1.0194	
1471	SRM	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [source:swissprot;acc:p19623]	221.412	217.199	1.0194	
1472	GARS	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [source:swissprot;acc:p41250]	221.412	217.199	1.0194	
1473	EARS2	glutamyl trna synthetase. [source:sptrembl;acc:o14563]	221.412	217.199	1.0194	
1474	RANBP5	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [source:swissprot;acc:o00410]	218.582	214.427	1.01938	
1475	KYNU	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	181.882	178.438	1.0193	
1476	RANBP6	ran-gtp binding protein (fragment). [source:sptrembl;acc:o60518]	218.591	214.457	1.01928	
1477		transformer-2 protein homolog (tra-2 alpha). [source:swissprot;acc:q13595]	215.328	211.267	1.01922	
1478	SFRS10	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [source:swissprot;acc:q15815]	215.122	211.066	1.01922	
1479	MPP6	maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [source:swissprot;acc:q9nzw5]	228.469	232.855	1.0192	

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/