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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2808 to 2857 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1404	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [source:swissprot;acc:q15427]	Divided	232.752	237.65	1.02104	
1405	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [source:swissprot;acc:q99613]	Divided	245.532	240.483	1.021	
1405	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_145245]	Subtracted	218.829	214.493	4.336	
1406	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_005665]	Subtracted	218.829	214.493	4.336	
1406	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	Divided	212.833	208.456	1.021	
1407	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [source:refseq;acc:nm_020830]	Divided	206.104	210.424	1.02096	
1407	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [source:refseq;acc:nm_020830]	Subtracted	206.104	210.424	4.32	
1408	stromal interaction molecule 1 precursor. [source:swissprot;acc:q13586]	Divided	206.102	210.42	1.02095	
1408	stromal interaction molecule 1 precursor. [source:swissprot;acc:q13586]	Subtracted	206.102	210.42	4.318	
1409	trap/mediator complex component trap25. [source:refseq;acc:nm_080651]	Divided	206.102	210.42	1.02095	
1409	trap/mediator complex component trap25. [source:refseq;acc:nm_080651]	Subtracted	206.102	210.42	4.318	
1410	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [source:swissprot;acc:o96013]	Subtracted	206.102	210.42	4.318	
1410	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [source:refseq;acc:nm_052950]	Divided	206.1	210.417	1.02095	
1411	polyposis locus protein 1 (tb2 protein). [source:swissprot;acc:q00765]	Subtracted	206.102	210.42	4.318	
1411	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [source:swissprot;acc:o96013]	Divided	206.102	210.42	1.02095	
1412	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [source:swissprot;acc:p11310]	Subtracted	206.102	210.42	4.318	
1412	polyposis locus protein 1 (tb2 protein). [source:swissprot;acc:q00765]	Divided	206.102	210.42	1.02095	
1413	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [source:swissprot;acc:p11310]	Divided	206.102	210.42	1.02095	
1413	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [source:refseq;acc:nm_138393]	Subtracted	206.102	210.42	4.318	
1414	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [source:refseq;acc:nm_138393]	Divided	206.102	210.42	1.02095	
1414	stromal interaction molecule 2 precursor. [source:swissprot;acc:q9p246]	Subtracted	206.102	210.42	4.318	
1415	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [source:swissprot;acc:q9p286]	Subtracted	206.102	210.42	4.318	
1415	stromal interaction molecule 2 precursor. [source:swissprot;acc:q9p246]	Divided	206.102	210.42	1.02095	
1416	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [source:swissprot;acc:q9p286]	Divided	206.102	210.42	1.02095	
1416	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [source:refseq;acc:nm_052950]	Subtracted	206.1	210.417	4.317	
1417	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [source:swissprot;acc:q13510]	Subtracted	207.076	211.391	4.315	
1417	carboxypeptidase a5. [source:refseq;acc:nm_080385]	Divided	203.979	208.229	1.02084	
1418	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	Divided	203.979	208.229	1.02084	
1418	cone-rod homeobox protein. [source:swissprot;acc:o43186]	Subtracted	244.331	240.061	4.27	
1419	homeobox protein otx1. [source:swissprot;acc:p32242]	Subtracted	244.367	240.098	4.269	
1419	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	Divided	203.979	208.229	1.02084	
1420	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [source:swissprot;acc:q03154]	Divided	203.979	208.229	1.02084	
1420	homeobox protein otx2. [source:swissprot;acc:p32243]	Subtracted	244.478	240.212	4.266	
1421	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [source:swissprot;acc:q13510]	Divided	207.076	211.391	1.02084	
1421	carboxypeptidase a5. [source:refseq;acc:nm_080385]	Subtracted	203.979	208.229	4.25	
1422	carboxypeptidase a1 precursor (ec 3.4.17.1). [source:swissprot;acc:p15085]	Divided	203.979	208.229	1.02084	
1422	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	Subtracted	203.979	208.229	4.25	
1423	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [source:swissprot;acc:p50238]	Divided	221.152	216.659	1.02074	
1423	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	Subtracted	203.979	208.229	4.25	
1424	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [source:swissprot;acc:q03154]	Subtracted	203.979	208.229	4.25	
1424	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [source:swissprot;acc:p05023]	Divided	214.717	219.157	1.02068	
1425	carboxypeptidase a1 precursor (ec 3.4.17.1). [source:swissprot;acc:p15085]	Subtracted	203.979	208.229	4.25	
1425	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [source:swissprot;acc:o60911]	Divided	214.717	219.157	1.02068	
1426	cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [source:swissprot;acc:p07711]	Divided	214.717	219.157	1.02068	
1426	protein cgi-147. [source:swissprot;acc:q9y3e5]	Subtracted	221.961	226.186	4.225	
1427	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	Subtracted	229.459	225.237	4.222	
1427	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]	Divided	214.717	219.157	1.02068	
1428	casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [source:swissprot;acc:p48729]	Subtracted	229.459	225.237	4.222	
1428	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	Divided	214.717	219.157	1.02068	
1429	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [source:swissprot;acc:p47897]	Subtracted	221.412	217.199	4.213	

Legend:
- Rank is the rank after comparing the two networks
- 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/