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 Value Type description Network Comparison Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 818 to 867 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	network_comparison	green	
818	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [source:swissprot;acc:q9nzl6]	168.592	1.04422	161.452	
819	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [source:swissprot;acc:p36954]	228.563	1.04421	238.668	
820	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [source:swissprot;acc:q9y399]	221.716	1.04413	231.501	
821	u3 snornp protein 4 homolog. [source:refseq;acc:nm_033416]	221.676	1.0441	231.453	
822	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [source:swissprot;acc:p55884]	243.067	1.04408	232.805	
823	transcription factor iib. [source:refseq;acc:nm_013242]	206.068	1.04354	197.471	
824	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [source:swissprot;acc:q12872]	206.068	1.04354	197.471	
825	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	206.214	1.04352	197.614	
826	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [source:swissprot;acc:q92993]	223.186	1.04335	213.912	
827	loh1cr12. [source:refseq;acc:nm_058169]	230.087	1.0431	220.579	
828	unr protein. [source:swissprot;acc:o75534]	230.087	1.0431	220.579	
829	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	135.844	1.04288	130.259	
830	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [source:refseq;acc:nm_004562]	231.734	1.0428	222.222	
831	hepatoma-derived growth factor-related protein 2. [source:refseq;acc:nm_032631]	231.734	1.0428	222.222	
832	cgi-142; hepatoma-derived growth factor 2. [source:refseq;acc:nm_016073]	231.734	1.0428	222.222	
833	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [source:refseq;acc:nm_033222]	231.734	1.0428	222.222	
834	60s ribosomal protein l8. [source:swissprot;acc:p25120]	231.734	1.0428	222.222	
835	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [source:swissprot;acc:p51858]	231.734	1.0428	222.222	
836	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	231.734	1.0428	222.222	
837	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	231.734	1.0428	222.222	
838	rw1 protein (fragment). [source:swissprot;acc:q92545]	231.734	1.0428	222.222	
839	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	177.776	1.04268	170.499	
840	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	198.781	1.04259	190.66	
841	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	198.781	1.04259	190.66	
842	jm1 protein. [source:refseq;acc:nm_014008]	219.762	1.04248	210.806	
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]	218.521	1.04244	227.796	
844	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	178.033	1.04223	170.82	
845	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	228.599	1.04193	219.399	
846	methyltransferase like 2. [source:refseq;acc:nm_018396]	147.211	1.04184	153.371	
847	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	147.211	1.04184	153.371	
848	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	147.211	1.04184	153.371	
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]	147.211	1.04184	153.371	
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]	107.842	1.04161	112.329	
851	trs85 homolog. [source:swissprot;acc:q9y2l5]	107.842	1.04161	112.329	
852	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	193.114	1.04154	185.412	
853	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	108.289	1.0414	112.772	
854	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	108.289	1.0414	112.772	
855	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	178.514	1.04138	171.42	
856	xenotropic and polytropic retrovirus receptor. [source:refseq;acc:nm_004736]	215.028	1.04068	206.623	
857	putatative 28 kda protein. [source:refseq;acc:nm_020143]	227.241	1.0406	236.467	
858	syntaxin 12. [source:refseq;acc:nm_177424]	217.446	1.04043	208.997	
859	60s ribosomal protein l39. [source:swissprot;acc:p02404]	234.025	1.04031	224.958	
860	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	234.025	1.04031	224.958	
861	40s ribosomal protein s19. [source:swissprot;acc:p39019]	234.025	1.04031	224.958	
862	60s ribosomal protein l31. [source:swissprot;acc:p12947]	234.025	1.04031	224.958	
863	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19138]	240.194	1.03999	230.957	
864	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19784]	240.194	1.03999	230.957	
865	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	211.961	1.03997	203.814	
866	signal recognition particle 68 kda protein (srp68). [source:swissprot;acc:q9uhb9]	221.306	1.03994	212.806	
867	40s ribosomal protein s3a. [source:swissprot;acc:p49241]	225.689	1.03981	234.674	

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/