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

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Showing element 1863 to 1912 of 3228 in total

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

red	green	Rank	description	network_comparison
5791.82	6340.86	1010	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	1.0948
		1011	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3]
		1012	actin binding lim protein 2. [refseq;acc:nm_032432]
		1013	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]
		1014	synapsin ii. [swissprot;acc:q92777]
		1015	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
		1016	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]
		1017	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
		1018	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]
		1019	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
		1020	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
		1021	synapsin i (brain protein 4.1). [swissprot;acc:p17600]
5792.08	6305.67	1126	importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131]	1.08867
5793.29	6248.51	1368	beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612]	1.07858
5793.47	6248.71	1367	megf10 protein. [refseq;acc:nm_032446]
5793.55	6248.79	1366	megf11 protein. [refseq;acc:nm_032445]
5794.8	6427.79	810	jm1 protein. [refseq;acc:nm_014008]	1.10923
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

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.