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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1412 to 1461 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
1412	REEP5	polyposis locus protein 1 (tb2 protein). [source:swissprot;acc:q00765]	206.102	210.42	1.02095	
1413	ACADM	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [source:swissprot;acc:p11310]	206.102	210.42	1.02095	
1414	REEP6	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [source:refseq;acc:nm_138393]	206.102	210.42	1.02095	
1415	STIM2	stromal interaction molecule 2 precursor. [source:swissprot;acc:q9p246]	206.102	210.42	1.02095	
1416	PAK7	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [source:swissprot;acc:q9p286]	206.102	210.42	1.02095	
1417	CPA5	carboxypeptidase a5. [source:refseq;acc:nm_080385]	203.979	208.229	1.02084	
1418	CPB1	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	203.979	208.229	1.02084	
1419	SLC3A1	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	203.979	208.229	1.02084	
1420	ACY1	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [source:swissprot;acc:q03154]	203.979	208.229	1.02084	
1421	ASAH1	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [source:swissprot;acc:q13510]	207.076	211.391	1.02084	
1422	CPA1	carboxypeptidase a1 precursor (ec 3.4.17.1). [source:swissprot;acc:p15085]	203.979	208.229	1.02084	
1423		cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [source:swissprot;acc:p50238]	221.152	216.659	1.02074	
1424	ATP1A1	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [source:swissprot;acc:p05023]	214.717	219.157	1.02068	
1425	CTSL2	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [source:swissprot;acc:o60911]	214.717	219.157	1.02068	
1426	CTSL1	cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [source:swissprot;acc:p07711]	214.717	219.157	1.02068	
1427	ATP1A3	sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [source:swissprot;acc:p13637]	214.717	219.157	1.02068	
1428	ATP1A2	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	214.717	219.157	1.02068	
1429	WDR26	wd repeat domain 26. [source:refseq;acc:nm_025160]	213.351	217.74	1.02057	
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	

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/