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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Value Type	Rank	Gene	Hugo	description	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 713 to 762 of 12912 in total

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

Rank	Hugo	description	red	green	network_comparison
713	NAT10	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	3996.81	4465.61	1.11729
714	no value	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	5222.71	5834.57	1.11715
715	EIF3M	dendritic cell protein. [refseq;acc:nm_006360]	6593.17	7364.55	1.117
716	CPXM2	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]
717	CPN1	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
718	CPZ	cpz gene product. [refseq;acc:nm_003652]
719	CPE	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]
720	CPXM1	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]
721	STX7	syntaxin 7. [swissprot;acc:o15400]	5580.97	6233.52	1.11692
722	HARS2	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	8061.05	9002.33	1.11677
723	HARS	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	8056.09	8996.46	1.11673
724	FARSA	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	5384.41	6012.82	1.11671
725	FARS2	phenylalanine-trna synthetase. [refseq;acc:nm_006567]
726	MLH3	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	6327.86	7064.13	1.11635
727	RPL24	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	7087.23	7911.25	1.11627
728	ASNSD1	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	6000.23	6696.89	1.11611
729	ATP6V1A	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]
730	ASNS	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
731	no value	methyltransferase like 2. [refseq;acc:nm_018396]	13241.4	11864	1.1161
732	DYNLT1	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
733	FZR1	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]
734	PCSK5	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]
735	ATP6V0C	vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449]	5768.32	6434.78	1.11554
736	SGCZ	sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167]
737	ACBD3	golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735]
738	SGCD	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629]
739	MARCH8	cellular modulator of immune recognition. [refseq;acc:nm_145021]
740	ATP6V0B	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437]
741	SGCG	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]
742	EIF3G	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821]	4131.04	4607.9	1.11543
743	EIF3A	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]
744	CTPS2	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	12515.4	11221.1	1.11535
745	NET1	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863]	4086.6	4557.68	1.11527
746	ARHGEF3	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]
747	UTP20	down-regulated in metastasis. [refseq;acc:nm_014503]
748	CTPS	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	12503.3	11212	1.11517
749	PCYT2	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	4565.34	5085.92	1.11403
750	MYL1	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976]
751	MYL3	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590]
752	NDUFS6	nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380]
753	MYL6	myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649]
754	no value	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]
755	NOL6	nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	4079.81	4545.01	1.11402
756	PAPD5	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	4725.28	5261.06	1.11339
757	SRP68	signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	5622.89	6260.02	1.11331
758	POLE2	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282]	3760.3	4185.82	1.11316
759	PFKP	6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813]	4254.62	4736.03	1.11315
760	ATP6V0D2	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]	5870.2	6533.39	1.11298
761	EIF5B	translation initiation factor if-2. [swissprot;acc:o60841]	5811.51	6467.62	1.1129
762	PMS2	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	6231.31	6933.9	1.11275

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
- Hugo is the HGNC identifier if it exists
- 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.