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

Results: HTML CSV LaTeX

Showing element 1880 to 1929 of 3228 in total

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

red	green	Rank	description	network_comparison
5795.13	6314.19	1115	5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707]	1.08957
5796.03	6243.78	1431	limkain beta 2. [refseq;acc:nm_025140]	1.07725
5797.88	6391.75	877	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	1.10243
		878	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
		879	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
5798.31	6230.55	1499	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	1.07455
5799.14	6255.04	1365	gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8]	1.07862
5799.29	6265.2	1331	transaldolase (ec 2.2.1.2). [swissprot;acc:p37837]	1.08034
5799.35	6305.95	1173	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	1.08735
		1175	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853]
		1176	aarf domain containing kinase 4. [refseq;acc:nm_024876]
		1177	aarf domain containing kinase 1. [refseq;acc:nm_020421]
5799.84	6122.18	2083	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	1.05558
5800.22	6122.6	2084
5800.93	6123.38	2082	ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792]	1.05559
5800.95	6355.71	994	interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9]	1.09563
5803.1	6256.03	1399	heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]	1.07805
5803.12	6256.05	1398	heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943]
5803.27	6256.23	1397	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597]
5803.45	6256.43	1400	heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942]
5803.54	6256.54	1396	g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849]	1.07806
5803.95	6269.44	1333	abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759]	1.0802
5804.75	6270.15	1334	spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470]	1.08018
5805.06	6158.16	1942	pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811]	1.06083
5807.83	6300.47	1234	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245]	1.08482
		1235	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
5811.51	6467.62	761	translation initiation factor if-2. [swissprot;acc:o60841]	1.1129
5812.02	6262.07	1411	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	1.07743
5813.84	6263.92	1412	histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6]	1.07742
5813.88	6263.96	1414	histone deacetylase 4 (hd4). [swissprot;acc:p56524]	1.07741
	6263.97	1413	histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]	1.07742
5815.14	6272.66	1364	protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312]	1.07868
5815.33	6265.44	1415	14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	1.0774
5816.12	6196.21	1809	epsin 3. [refseq;acc:nm_017957]	1.06535
5817.07	6138.59	2090	kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685]	1.05527
5817.41	6138.8	2092	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	1.05525
5817.56	6138.9	2093	fuse binding protein 3 (fragment). [sptrembl;acc:q92946]	1.05524
5819.36	6092.93	2247	rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062]	1.04701
5819.37	6239.55	1569	traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614]	1.0722
5819.39	6244.37	1546	26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	1.07303
5822.25	6242.94	1567	26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	1.07226
5825.61	6126.74	2170	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	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]
5826	6195.48	1883	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	1.06342
		1884	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]
		1885	ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]
		1886	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]
5826.29	6335.93	1171	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	1.08747
5826.32	6335.95	1172	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]

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.