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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3414 to 3463 of 8289 in total 
Network Comparison Type	Divided
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Interaction Map	red	green	network_comparison	
1707	BUB1B	mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [source:swissprot;acc:o60566]	High confidence	221.283	218.334	1.01351	
1708	NPC2	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [source:swissprot;acc:q15668]	Low confidence	200.171	196.144	1.02053	
1708	PNPO	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	High confidence	221.283	218.334	1.01351	
1709	HHEX	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [source:swissprot;acc:q03014]	High confidence	198.014	195.385	1.01346	
1709	NOL6	nucleolar rna-associated protein alpha isoform. [source:refseq;acc:nm_022917]	Low confidence	201.868	197.808	1.02052	
1710		casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [source:swissprot;acc:p49674]	High confidence	227.225	224.21	1.01345	
1710	SCFD1	vesicle transport-related protein isoform a; vesicle transport-related protein. [source:refseq;acc:nm_016106]	Low confidence	201.891	197.832	1.02052	
1711	HLCS	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [source:swissprot;acc:p50747]	High confidence	218.436	215.553	1.01337	
1711	PABPC1	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [source:swissprot;acc:p11940]	Low confidence	204.279	200.171	1.02052	
1712	CLK1	protein kinase clk1 (ec 2.7.1.-) (clk). [source:swissprot;acc:p49759]	Low confidence	201.754	197.698	1.02052	
1712	TAF11	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [source:swissprot;acc:q15544]	High confidence	208.598	211.375	1.01331	
1713	AGL	glycogen debranching enzyme (glycogen debrancher) [includes: 4-alpha- glucanotransferase (ec 2.4.1.25) (oligo-1,4-1,4-glucantransferase); amylo-alpha-1,6-glucosidase (ec 3.2.1.33) (amylo-1,6-glucosidase) (dextrin 6-alpha-d-glucosidase)]. [source:swissprot;acc:p35573]	Low confidence	194.18	190.277	1.02051	
1713	SH3GL3	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	High confidence	206.823	204.111	1.01329	
1714	ARMET	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	High confidence	206.549	203.844	1.01327	
1714	LTB4DH	nadp-dependent leukotriene b4 12-hydroxydehydrogenase (ec 1.1.1.-). [source:swissprot;acc:q14914]	Low confidence	197.526	193.557	1.02051	
1715		ubiquitin. [source:swissprot;acc:p02248]	Low confidence	204.321	200.214	1.02051	
1715	HDC	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	High confidence	206.549	203.844	1.01327	
1716	DPM1	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	Low confidence	200.933	196.894	1.02051	
1716	SH3GL2	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [source:swissprot;acc:q99962]	High confidence	206.522	203.818	1.01327	
1717	CLK4	protein serine threonine kinase clk4. [source:refseq;acc:nm_020666]	Low confidence	201.747	197.695	1.0205	
1717	OSGEP	o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	High confidence	221.058	218.164	1.01327	
1718	SH3GL1	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	High confidence	206.251	203.553	1.01325	
1718	UBE2J2	ubiquitin conjugating enzyme 6; ubiquitin-conjugating enzyme e2, j2. [source:refseq;acc:nm_058167]	Low confidence	201.429	197.384	1.02049	
1719		helicase (fragment). [source:sptrembl;acc:q92771]	High confidence	187.204	189.679	1.01322	
1719	TBK1	tank-binding kinase 1; nf-kb-activating kinase. [source:refseq;acc:nm_013254]	Low confidence	204.39	200.288	1.02048	
1720	DDX12	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	High confidence	187.205	189.679	1.01322	
1720	MCC	colorectal mutant cancer protein (mcc protein). [source:swissprot;acc:p23508]	Low confidence	204.39	200.288	1.02048	
1721	CSNK1D	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [source:swissprot;acc:p48730]	High confidence	227.125	224.164	1.01321	
1721	IKBKE	inhibitor of nuclear factor kappa-b kinase epsilon subunit (ec 2.7.1.-) (i kappa-b kinase epsilon) (ikbke) (ikk-epsilon) (ikk-e) (inducible i kappa-b kinase) (ikk-i). [source:swissprot;acc:q14164]	Low confidence	204.39	200.288	1.02048	
1722	CCNB2	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	Low confidence	201.688	197.642	1.02047	
1722	RPS13	40s ribosomal protein s13. [source:swissprot;acc:q02546]	High confidence	220.899	223.813	1.01319	
1723	NADK	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [source:swissprot;acc:o95544]	High confidence	212.36	215.147	1.01312	
1723	XPO5	exportin 5. [source:refseq;acc:nm_020750]	Low confidence	202.615	198.551	1.02047	
1724	DNAJC5B	dnaj homolog subfamily c member x (beta cysteine string protein) (beta-csp). [source:swissprot;acc:q9uf47]	Low confidence	193.723	189.838	1.02046	
1724	IPMK	inositol polyphosphate multikinase. [source:refseq;acc:nm_152230]	High confidence	217.676	220.53	1.01311	
1725	AFG3L2	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [source:swissprot;acc:q9y4w6]	High confidence	217.676	220.53	1.01311	
1725	DNAJC5	dnaj homolog subfamily c member 5 (cysteine string protein) (csp). [source:swissprot;acc:q9h3z4]	Low confidence	193.719	189.835	1.02046	
1726	FUT8	alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [source:swissprot;acc:q9byc5]	High confidence	217.676	220.53	1.01311	
1726	NCK1	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [source:swissprot;acc:p16333]	Low confidence	200.211	196.199	1.02045	
1727	IMPA1	inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [source:swissprot;acc:p29218]	High confidence	210.366	213.118	1.01308	
1727	POLR1E	rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	Low confidence	201.68	197.639	1.02045	
1728	IMPA2	inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [source:swissprot;acc:o14732]	High confidence	210.358	213.103	1.01305	
1728	SCP2	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [source:swissprot;acc:p22307]	Low confidence	201.514	197.476	1.02045	
1729	ATG12	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	High confidence	187.582	190.028	1.01304	
1729	PIN4	peptidyl-prolyl cis-trans isomerase nima-interacting 4 (ec 5.2.1.8) (rotamase pin4) (ppiase pin4) (parvulin 14) (par14) (peptidyl-prolyl cis/trans isomerase epvh) (hpar14). [source:swissprot;acc:q9y237]	Low confidence	201.514	197.476	1.02045	
1730	CABC1	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [source:swissprot;acc:q8ni60]	High confidence	215.336	212.567	1.01303	
1730	OSGEP	o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	Low confidence	194.383	190.487	1.02045	
1731	ADCK2	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [source:refseq;acc:nm_052853]	High confidence	215.336	212.567	1.01303	
1731	HOXA7	homeobox protein hox-a7 (hox-1a) (hox 1.1). [source:swissprot;acc:p31268]	Low confidence	203.115	199.047	1.02044	
1732		basic proline-rich peptide p-e (ib-9). [source:swissprot;acc:p02811]	Low confidence	201.552	197.517	1.02043	

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/