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

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Showing element 2751 to 2800 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
2751	PSMA1	proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786]	215.338	215.312	1.00012
2752	TP53RK	p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44]	221.7	221.716	1.00007
2753	AGXT	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549]	208.859	208.846	1.00006
2754	MTHFS	5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914]	210.638	210.642	1.00002
2755	DHPS	deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366]	212.403	212.401	1.00001
2756	no value	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	0.00001	0.00001	1
2757	NAP1L1	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
2758	NAP1L2	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
2759	RXRA	retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
2760	TAL2	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
2761	GNB1L	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]
2762	DRG1	developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295]
2763	PCGF3	ring finger protein 3. [refseq;acc:nm_006315]
2764	RAB11B	ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]
2765	no value	histone h2a.e (h2a/e). [swissprot;acc:q99878]
2766	SS18L1	ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]
2767	no value	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
2768	HIST2H2AB	histone h2a.x (h2a/x). [swissprot;acc:p16104]
2769	HIST2H2AC	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]
2770	NIPSNAP1	nipsnap1 protein. [swissprot;acc:q9bpw8]
2771	TBX1	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]
2772	NUDT14	uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]
2773	BMP8A	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
2774	C3orf37	dc12 protein. [refseq;acc:nm_020187]
2775	JRKL	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]
2776	BCOR	bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745]
2777	RABIF	guanine nucleotide exchange factor mss4 (rab interacting factor). [swissprot;acc:p47224]
2778	MAFA	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [sptrembl;acc:q8nhw3]
2779	CAV3	caveolin-3 (m-caveolin). [swissprot;acc:p56539]
2780	KPNA2	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]
2781	EXOC7	exocyst complex component exo70. [swissprot;acc:q9upt5]
2782	ATP6AP2	vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [swissprot;acc:o75787]
2783	MAB21L2	mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439]
2784	HIST3H2A	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
2785	NPM1	nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748]
2786	MAB21L1	mab-21-like protein 1; mab-21-like 1. [refseq;acc:nm_005584]
2787	HMG4L	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]
2788	AKAP5	a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588]
2789	PTPN11	protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [swissprot;acc:q06124]
2790	no value	transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3]
2791	COX5A	cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674]
2792	MAF	transcription factor maf (proto-oncogene c-maf). [swissprot;acc:o75444]
2793	no value	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]
2794	SH2B1	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]
2795	NDUFV2	nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404]
2796	DMAP1	dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5]
2797	ODF3	sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280]
2798	ARIH2	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]
2799	HMGB4	hmg2 like. [refseq;acc:nm_145205]
2800	MLXIP	mondoa. [refseq;acc:nm_014938]

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.