MK5 Microarray Data

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

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Showing element 825 to 874 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
825	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	206.214	197.614	1.04352
826	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993]	223.186	213.912	1.04335
827	loh1cr12. [refseq;acc:nm_058169]	230.087	220.579	1.0431
828	unr protein. [swissprot;acc:o75534]
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). [swissprot;acc:o43236]	135.844	130.259	1.04288
830	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	231.734	222.222	1.0428
831	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
832	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
833	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]
834	60s ribosomal protein l8. [swissprot;acc:p25120]
835	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]
836	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]
837	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]
838	rw1 protein (fragment). [swissprot;acc:q92545]
839	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	177.776	170.499	1.04268
840	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]	198.781	190.66	1.04259
841	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]
842	jm1 protein. [refseq;acc:nm_014008]	219.762	210.806	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)]. [swissprot;acc:p22102]	218.521	227.796	1.04244
844	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	178.033	170.82	1.04223
845	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	228.599	219.399	1.04193
846	methyltransferase like 2. [refseq;acc:nm_018396]	147.211	153.371	1.04184
847	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
848	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]
849	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]
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. [refseq;acc:nm_006693]	107.842	112.329	1.04161
851	trs85 homolog. [swissprot;acc:q9y2l5]
852	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	193.114	185.412	1.04154
853	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	108.289	112.772	1.0414
854	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
855	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	178.514	171.42	1.04138
856	xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	215.028	206.623	1.04068
857	putatative 28 kda protein. [refseq;acc:nm_020143]	227.241	236.467	1.0406
858	syntaxin 12. [refseq;acc:nm_177424]	217.446	208.997	1.04043
859	60s ribosomal protein l39. [swissprot;acc:p02404]	234.025	224.958	1.04031
860	60s ribosomal protein l18a. [swissprot;acc:q02543]
861	40s ribosomal protein s19. [swissprot;acc:p39019]
862	60s ribosomal protein l31. [swissprot;acc:p12947]
863	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	240.194	230.957	1.03999
864	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
865	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	211.961	203.814	1.03997
866	signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	221.306	212.806	1.03994
867	40s ribosomal protein s3a. [swissprot;acc:p49241]	225.689	234.674	1.03981
868	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	233.298	242.571	1.03975
869	exocyst complex component sec8. [swissprot;acc:q96a65]	217.762	209.449	1.03969
870	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	211.908	203.832	1.03962
871	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	110.2	114.552	1.03949
872	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	224.413	233.272	1.03948
873	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]
874	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	212.002	203.954	1.03946

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.