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 2125 to 2174 of 12912 in total

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

Rank	Hugo	description	red	green	network_comparison
2125	RPS27L	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	4806.38	5067	1.05422
2126	no value	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	4806.33	5066.92
2127	EIF3K	eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5]	5328.73	5616.59	1.05402
2128	SLMO1	erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584]
2129	BBS7	bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824]
2130	no value	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]
2131		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
2132	SLMO2	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]
2133	EIF3EIP	eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262]
2134	RBM7	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]
2135	EXOC3	exocyst complex component sec6. [swissprot;acc:o60645]	7387.42	7785.45	1.05388
2136	RPL19	60s ribosomal protein l19. [swissprot;acc:p14118]	3687.49	3499.2	1.05381
2137	SH3BGR	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	5859.1	6173.7	1.05369
2138	OXR1	oxidation resistance 1. [refseq;acc:nm_181354]
2139	LATS2	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]
2140	DYM	dymeclin. [refseq;acc:nm_017653]
2141	SH3BGRL	sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]
2142	LATS1	lats homolog 1. [refseq;acc:nm_004690]
2143	no value	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
2144	NCOA7	nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]
2145	C20orf118	dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]
2146	TBC1D22B	tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]
2147	TBC1D22A	tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]
2148	DCTD	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	4644.58	4892.06	1.05328
2149	TNPO1	importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973]	5778.62	6086.03	1.0532
2150	TNPO2	karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433]	5779.82	6086.64	1.05308
2151	EEA1	early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566]	4871.11	5129.63	1.05307
2152	RPS23	40s ribosomal protein s23. [swissprot;acc:p39028]	3560.63	3381.34	1.05302
2153	MRPS12	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
2154	ACOX2	acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424]	6884.69	7247.36	1.05268
2155	CENTG2	centaurin gamma 2. [swissprot;acc:q9upq3]	5701.81	6000.03	1.0523
2156	USO1	general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763]
2157	CENTG1	centaurin gamma 1. [swissprot;acc:q99490]
2158	CENTG3	centaurin gamma 3. [swissprot;acc:q96p47]
2159	ACVR1B	serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896]	5379.49	5660.18	1.05218
2160	ACVR1C	activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]	5379.55	5660.25
2161	FREQ	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610]	5379.33	5660
2162	TGFBR1	tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897]	5379.03	5659.64	1.05217
2163	POLR2A	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	3569.06	3392.22	1.05213
2164	COQ6	ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9]	6952.66	7315.06	1.05212
2165	KMO	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]
2166	SQLE	squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534]
2167	MRPL3	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	3641.62	3461.4	1.05207
2168	HAO1	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8]	4561.75	4799.24	1.05206
2169	RPL5	60s ribosomal protein l5. [swissprot;acc:p46777]	3639.65	3459.64	1.05203
2170	EXO1	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	5825.61	6126.74	1.05169
2171	FANCL	phd finger protein 9. [refseq;acc:nm_018062]
2172	SOLH	small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
2173	CDH1	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	3641.4	3462.96	1.05153
2174	no value	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	3641.45	3463.02	1.05152

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.