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	Value Type	description	Rank	network_comparison	green	Filtered	red	Interaction Map

Results: HTML CSV LaTeX

Showing element 2827 to 2876 of 3228 in total

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

description	Rank	network_comparison	green	red
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]	1024	1.03195	199.266	205.632
thousand and one amino acid protein kinase. [refseq;acc:nm_004783]	2906	1	0.00001	0.00001
thrombospondin 3 precursor. [swissprot;acc:p49746]	227	1.12186	269.234	239.99
thymic stromal co-transporter. [refseq;acc:nm_033051]	472	1.07686	267.226	248.152
thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]	2837	1	0.00001	0.00001
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	2104	1.00729	207.813	209.328
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818]	1590	1.01621	228.769	225.119
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	2703	1.00066	188.311	188.435
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669]	1460	1.0196	209.851	205.817
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]	1621	1.01521	225.185	228.611
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	2816	1	0.00001	0.00001
tigger transposable element derived 6. [refseq;acc:nm_030953]	2853
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	2944
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	133	1.2069	290	350
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	132
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603]	2540	1.00205	216.699	217.144
topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027]	2642	1.00119	194.328	194.097
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	2073	1.00806	227.433	229.267
trabid protein. [swissprot;acc:q9ugi0]	3210	1	0.00001	0.00001
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614]	2031	1.00879	216.562	218.466
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	2322	1.00476	234.905	236.023
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837]	2364	1.00414	213.697	212.816
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	1619	1.01527	231.246	227.768
transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560]	1618
transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [swissprot;acc:q99081]	2948	1	0.00001	0.00001
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	2940
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275]	2279	1.00538	190.909	191.936
transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549]	2969	1	0.00001	0.00001
transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481]	3220
transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [swissprot;acc:q92754]	3164
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	865	1.03997	203.814	211.961
transcription factor btf3 homolog 3. [swissprot;acc:q13892]	870	1.03962	203.832	211.908
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	1192	1.02558	215.237	220.742
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	406	1.08731	244.304	265.634
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	374	1.09436	244.168	267.208
transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [swissprot;acc:p15923]	3182	1	0.00001	0.00001
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	384	1.09083	244.236	266.421
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	385
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]	666	1.0577	216.576	229.072
transcription factor iib. [refseq;acc:nm_013242]	823	1.04354	197.471	206.068
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	2486	1.00287	218.72	218.093
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	478	1.07409	212.321	228.051
transcription factor jun-b. [swissprot;acc:p17275]	53	1.26611	158.868	201.144
transcription factor jun-d. [swissprot;acc:p17535]	54	1.26425	158.941	200.941
transcription factor lbx1. [swissprot;acc:p52954]	157	1.19466	298.263	249.663
transcription factor maf (proto-oncogene c-maf). [swissprot;acc:o75444]	2792	1	0.00001	0.00001
transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3]	2790
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9]	2737	1.00022	198.321	198.278
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	2736
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	2738

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.