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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 830 to 879 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
830	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [source:refseq;acc:nm_004562]	222.222	231.734	1.0428	
831	hepatoma-derived growth factor-related protein 2. [source:refseq;acc:nm_032631]	222.222	231.734	1.0428	
832	cgi-142; hepatoma-derived growth factor 2. [source:refseq;acc:nm_016073]	222.222	231.734	1.0428	
833	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [source:refseq;acc:nm_033222]	222.222	231.734	1.0428	
834	60s ribosomal protein l8. [source:swissprot;acc:p25120]	222.222	231.734	1.0428	
835	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [source:swissprot;acc:p51858]	222.222	231.734	1.0428	
836	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	222.222	231.734	1.0428	
837	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	222.222	231.734	1.0428	
838	rw1 protein (fragment). [source:swissprot;acc:q92545]	222.222	231.734	1.0428	
839	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	170.499	177.776	1.04268	
840	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	190.66	198.781	1.04259	
841	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	190.66	198.781	1.04259	
842	jm1 protein. [source:refseq;acc:nm_014008]	210.806	219.762	1.04248	
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]	227.796	218.521	1.04244	
844	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	170.82	178.033	1.04223	
845	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	219.399	228.599	1.04193	
846	methyltransferase like 2. [source:refseq;acc:nm_018396]	153.371	147.211	1.04184	
847	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	153.371	147.211	1.04184	
848	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	153.371	147.211	1.04184	
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]	153.371	147.211	1.04184	
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]	112.329	107.842	1.04161	
851	trs85 homolog. [source:swissprot;acc:q9y2l5]	112.329	107.842	1.04161	
852	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	185.412	193.114	1.04154	
853	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	112.772	108.289	1.0414	
854	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	112.772	108.289	1.0414	
855	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	171.42	178.514	1.04138	
856	xenotropic and polytropic retrovirus receptor. [source:refseq;acc:nm_004736]	206.623	215.028	1.04068	
857	putatative 28 kda protein. [source:refseq;acc:nm_020143]	236.467	227.241	1.0406	
858	syntaxin 12. [source:refseq;acc:nm_177424]	208.997	217.446	1.04043	
859	60s ribosomal protein l39. [source:swissprot;acc:p02404]	224.958	234.025	1.04031	
860	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	224.958	234.025	1.04031	
861	40s ribosomal protein s19. [source:swissprot;acc:p39019]	224.958	234.025	1.04031	
862	60s ribosomal protein l31. [source:swissprot;acc:p12947]	224.958	234.025	1.04031	
863	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19138]	230.957	240.194	1.03999	
864	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19784]	230.957	240.194	1.03999	
865	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	203.814	211.961	1.03997	
866	signal recognition particle 68 kda protein (srp68). [source:swissprot;acc:q9uhb9]	212.806	221.306	1.03994	
867	40s ribosomal protein s3a. [source:swissprot;acc:p49241]	234.674	225.689	1.03981	
868	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [source:swissprot;acc:p53602]	242.571	233.298	1.03975	
869	exocyst complex component sec8. [source:swissprot;acc:q96a65]	209.449	217.762	1.03969	
870	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	203.832	211.908	1.03962	
871	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	114.552	110.2	1.03949	
872	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [source:swissprot;acc:q07244]	233.272	224.413	1.03948	
873	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [source:swissprot;acc:o43172]	233.272	224.413	1.03948	
874	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	203.954	212.002	1.03946	
875	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [source:swissprot;acc:p54646]	203.954	212.002	1.03946	
876	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [source:swissprot;acc:q13131]	203.954	212.002	1.03946	
877	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	203.954	212.002	1.03946	
878	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	203.954	212.002	1.03946	
879	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	203.954	212.002	1.03946	

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/