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 3330 to 3379 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
833	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Squared	21455.4	24895.7	1.16035
	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376]	Rooted	59.7298	63.5169	1.0634
	zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]	Measured	4489.72	4965.35	1.10594
834	60s ribosomal protein l8. [swissprot;acc:p25120]	Ranked	231.734	222.222	1.0428
	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705]	Measured	5623.18	6218.77	1.10592
	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	Rooted	62.309	58.5957	1.06337
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Squared	31100.2	36086.5	1.16033
835	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]	Measured	5623.18	6218.77	1.10592
	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	Ranked	231.734	222.222	1.0428
	keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062]	Squared	31100.2	36086.5	1.16033
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Rooted	120.033	112.905	1.06313
836	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	Measured	4049	4477.43	1.10581
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Squared	31100.2	36086.5	1.16033
	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	Rooted	65.0565	69.1533	1.06297
	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	Ranked	231.734	222.222	1.0428
837	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	Measured	4063.64	4492.98	1.10565
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Squared	31100.2	36086.5	1.16033
	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	Ranked	231.734	222.222	1.0428
	tubby protein homolog. [swissprot;acc:p50607]	Rooted	65.0565	69.1533	1.06297
838	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Squared	31100.1	36086.4	1.16033
	pbk1 protein. [sptrembl;acc:o76021]	Measured	4064.23	4493.36	1.10559
	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]	Rooted	65.0565	69.1533	1.06297
	rw1 protein (fragment). [swissprot;acc:q92545]	Ranked	231.734	222.222	1.0428
839	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	Measured	7093.86	7842.67	1.10556
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Squared	31100.1	36086.4	1.16033
	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	Rooted	65.0565	69.1533	1.06297
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	Ranked	177.776	170.499	1.04268
840	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Squared	31100.1	36086.4	1.16033
	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]	Ranked	198.781	190.66	1.04259
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Measured	5786.67	6395.78	1.10526
	tbc1 domain family member 5. [swissprot;acc:q92609]	Rooted	65.0565	69.1533	1.06297
841	keratin associated protein 1.5. [refseq;acc:nm_031957]	Squared	31100.2	36086.5	1.16033
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	Measured	5786.67	6395.78	1.10526
	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]	Ranked	198.781	190.66	1.04259
	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]	Rooted	65.0565	69.1533	1.06297
842	jm1 protein. [refseq;acc:nm_014008]	Ranked	219.762	210.806	1.04248
	loh1cr12. [refseq;acc:nm_058169]	Measured	5195.48	5741.63	1.10512
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Squared	31100.1	36086.4	1.16033
	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]	Rooted	65.0565	69.1533	1.06297
843	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]	Squared	31100.2	36086.5	1.16033
	numb-like protein (numb-r). [swissprot;acc:q9y6r0]	Rooted	65.0565	69.1533	1.06297
	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]	Ranked	218.521	227.796	1.04244
	unr protein. [swissprot;acc:o75534]	Measured	5195.48	5741.63	1.10512
844	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	Ranked	178.033	170.82	1.04223
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Squared	31100.2	36086.5	1.16033
	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	Measured	6276.97	6934.8	1.1048
	tubby related protein 3 (tubby-like protein 3). [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). [swissprot;acc:q9ubs4]	Measured	6276.97	6934.8	1.1048
	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]	Squared	31100.1	36086.4	1.16033
	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	Ranked	228.599	219.399	1.04193

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.