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 2132 to 2181 of 3228 in total

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

Rank	description	red	green	network_comparison
2132	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	5328.73	5616.59	1.05402
2133	eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262]
2134	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]
2135	exocyst complex component sec6. [swissprot;acc:o60645]	7387.42	7785.45	1.05388
2136	60s ribosomal protein l19. [swissprot;acc:p14118]	3687.49	3499.2	1.05381
2137	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	oxidation resistance 1. [refseq;acc:nm_181354]
2139	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]
2140	dymeclin. [refseq;acc:nm_017653]
2141	sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]
2142	lats homolog 1. [refseq;acc:nm_004690]
2143	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
2144	nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]
2145	dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]
2146	tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]
2147	tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]
2148	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	4644.58	4892.06	1.05328
2149	importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973]	5778.62	6086.03	1.0532
2150	karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433]	5779.82	6086.64	1.05308
2151	early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566]	4871.11	5129.63	1.05307
2152	40s ribosomal protein s23. [swissprot;acc:p39028]	3560.63	3381.34	1.05302
2153	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
2154	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	centaurin gamma 2. [swissprot;acc:q9upq3]	5701.81	6000.03	1.0523
2156	general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763]
2157	centaurin gamma 1. [swissprot;acc:q99490]
2158	centaurin gamma 3. [swissprot;acc:q96p47]
2159	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	activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]	5379.55	5660.25
2161	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610]	5379.33	5660
2162	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	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	3569.06	3392.22	1.05213
2164	ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9]	6952.66	7315.06	1.05212
2165	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]
2166	squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534]
2167	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	3641.62	3461.4	1.05207
2168	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8]	4561.75	4799.24	1.05206
2169	60s ribosomal protein l5. [swissprot;acc:p46777]	3639.65	3459.64	1.05203
2170	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	phd finger protein 9. [refseq;acc:nm_018062]
2172	small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
2173	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	3641.4	3462.96	1.05153
2174	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
2175	60s ribosomal protein l23a. [swissprot;acc:p29316]	3642.13	3463.88	1.05146
2176	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	6674.58	7015.93	1.05114
2177	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	5887.43	6187.82	1.05102
2178	elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717]	5893.23	6193.33	1.05092
2179	elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378]	5896.51	6196.59	1.05089
2180	elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926]	5900.25	6200.24	1.05084
2181	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	4915.05	5164.75	1.0508

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.