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 3358 to 3407 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
840	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	Ranked	198.781	190.66	1.04259	
840	poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	Measured	5786.67	6395.78	1.10526	
840	tbc1 domain family member 5. [source:swissprot;acc:q92609]	Rooted	65.0565	69.1533	1.06297	
841	keratin associated protein 1.5. [source:refseq;acc:nm_031957]	Squared	31100.2	36086.5	1.16033	
841	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Measured	5786.67	6395.78	1.10526	
841	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Ranked	198.781	190.66	1.04259	
841	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	Rooted	65.0565	69.1533	1.06297	
842	jm1 protein. [source:refseq;acc:nm_014008]	Ranked	219.762	210.806	1.04248	
842	loh1cr12. [source:refseq;acc:nm_058169]	Measured	5195.48	5741.63	1.10512	
842	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	Squared	31100.1	36086.4	1.16033	
842	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	Rooted	65.0565	69.1533	1.06297	
843	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [source:swissprot;acc:o75690]	Squared	31100.2	36086.5	1.16033	
843	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	Rooted	65.0565	69.1533	1.06297	
843	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [source:swissprot;acc:p22102]	Ranked	218.521	227.796	1.04244	
843	unr protein. [source:swissprot;acc:o75534]	Measured	5195.48	5741.63	1.10512	
844	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Ranked	178.033	170.82	1.04223	
844	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	Squared	31100.2	36086.5	1.16033	
844	preimplantation protein 3; likely ortholog of preimplantation protein 3. [source:refseq;acc:nm_015387]	Measured	6276.97	6934.8	1.1048	
844	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	Rooted	65.0565	69.1533	1.06297	
845	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [source:swissprot;acc:q9ubs4]	Measured	6276.97	6934.8	1.1048	
845	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [source:swissprot;acc:q9nsy2]	Squared	31100.1	36086.4	1.16033	
845	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	Ranked	228.599	219.399	1.04193	
845	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	Rooted	65.0565	69.1533	1.06297	
846	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]	Measured	5607.43	6194.98	1.10478	
846	keratin associated protein 4.4. [source:refseq;acc:nm_032524]	Squared	31100.2	36086.5	1.16033	
846	methyltransferase like 2. [source:refseq;acc:nm_018396]	Ranked	147.211	153.371	1.04184	
846	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	Rooted	65.0565	69.1533	1.06297	
847	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	Squared	31100.1	36086.4	1.16033	
847	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Ranked	147.211	153.371	1.04184	
847	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	Measured	6776.85	7485.55	1.10458	
847	wd-repeat protein bing4. [source:swissprot;acc:o15213]	Rooted	51.7527	55.0117	1.06297	
848	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Ranked	147.211	153.371	1.04184	
848	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [source:swissprot;acc:p48059]	Squared	31100.1	36086.4	1.16033	
848	protein bap28. [source:swissprot;acc:q9h583]	Rooted	51.1817	54.4034	1.06295	
848	wd-repeat protein bing4. [source:swissprot;acc:o15213]	Measured	4066.56	4491.65	1.10453	
849	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [source:swissprot;acc:q16531]	Measured	6194.15	6839.37	1.10417	
849	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [source:swissprot;acc:q13418]	Squared	31100.1	36086.4	1.16033	
849	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Ranked	147.211	153.371	1.04184	
849	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Rooted	124.41	117.043	1.06294	
850	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [source:refseq;acc:nm_006693]	Ranked	107.842	112.329	1.04161	
850	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [source:swissprot;acc:p05166]	Measured	6194.15	6839.37	1.10417	
850	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Rooted	124.41	117.043	1.06294	
850	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [source:swissprot;acc:q96dr4]	Squared	31100.1	36086.4	1.16033	
851	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19138]	Measured	4307.12	4755.03	1.10399	
851	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Rooted	65.1512	69.252	1.06294	
851	ras suppressor protein 1 (rsu-1) (rsp-1). [source:swissprot;acc:q15404]	Squared	31100.1	36086.4	1.16033	
851	trs85 homolog. [source:swissprot;acc:q9y2l5]	Ranked	107.842	112.329	1.04161	
852	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19784]	Measured	4307.12	4755.03	1.10399	
852	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	Ranked	193.114	185.412	1.04154	
852	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	Rooted	58.5869	62.2732	1.06292	

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/