Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 2901 to 2950 of 3228 in total

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

description	Rank	red	green	network_comparison	
transcription termination factor, rna polymerase ii; lodestar protein. [source:refseq;acc:nm_003594]	3043	0.00001	0.00001	1	
transcriptional adapter 2-like (ada2-like protein) (kl04p). [source:swissprot;acc:o75478]	2746	201.476	201.514	1.00019	
transcriptional adaptor 3-like isoform a. [source:refseq;acc:nm_006354]	2744	201.476	201.514	1.00019	
transcriptional co-activator with pdz-binding motif (taz). [source:refseq;acc:nm_015472]	1991	219.26	217.194	1.00951	
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	266	241.07	267.88	1.11121	
transcriptional coactivator tubedown-100 isoform 1; putative n-acetyltransferase; gastric cancer antigen ga19. [source:refseq;acc:nm_057175]	2854	0.00001	0.00001	1	
transcriptional repressor nac1. [source:refseq;acc:nm_052876]	2872	0.00001	0.00001	1	
transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [source:swissprot;acc:q12986]	3169	0.00001	0.00001	1	
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [source:swissprot;acc:o60907]	2524	201.96	201.488	1.00234	
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	2526	201.96	201.488	1.00234	
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [source:swissprot;acc:q9y4p3]	2722	219.308	219.214	1.00043	
transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	887	244.155	234.96	1.03913	
transducin-like enhancer protein 1 (esg1). [source:swissprot;acc:q04724]	1172	219.375	213.767	1.02623	
transducin-like enhancer protein 2 (esg2). [source:swissprot;acc:q04725]	1166	219.374	213.759	1.02627	
transducin-like enhancer protein 3 (esg3). [source:swissprot;acc:q04726]	1165	219.401	213.785	1.02627	
transducin-like enhancer protein 4. [source:swissprot;acc:q04727]	1164	219.438	213.818	1.02628	
transformer-2 protein homolog (tra-2 alpha). [source:swissprot;acc:q13595]	1477	215.328	211.267	1.01922	
transforming growth factor beta 1 precursor (tgf-beta 1). [source:swissprot;acc:p01137]	3105	0.00001	0.00001	1	
transforming growth factor beta 2 precursor (tgf-beta 2) (glioblastoma-derived t-cell suppressor factor) (g-tsf) (bsc-1 cell growth inhibitor) (polyergin) (cetermin). [source:swissprot;acc:p08112]	3155	0.00001	0.00001	1	
transforming growth factor beta 3 precursor (tgf-beta 3). [source:swissprot;acc:p10600]	3035	0.00001	0.00001	1	
transforming protein n-ras. [source:swissprot;acc:p01111]	2682	144.427	144.564	1.00095	
transforming protein p21/h-ras-1 (c-h-ras). [source:swissprot;acc:p01112]	2680	144.422	144.56	1.00096	
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [source:swissprot;acc:p01116]	2670	144.391	144.538	1.00102	
transforming protein rhoa (h12). [source:swissprot;acc:p06749]	1026	205.632	199.266	1.03195	
transforming protein rhoc (h9). [source:swissprot;acc:p08134]	1023	205.632	199.266	1.03195	
transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [source:swissprot;acc:p55072]	2206	215.571	214.19	1.00645	
transketolase (ec 2.2.1.1) (tk). [source:swissprot;acc:p29401]	2103	214.666	216.236	1.00731	
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [source:swissprot;acc:p51854]	2527	209.143	208.659	1.00232	
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q14232]	2419	218.2	218.984	1.00359	
translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [source:swissprot;acc:p49770]	2049	220.787	222.634	1.00837	
translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q9ui10]	1866	221.725	224.133	1.01086	
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q13144]	1854	222.215	224.637	1.0109	
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q9nr50]	1857	222.215	224.637	1.0109	
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [source:swissprot;acc:p46199]	2397	210.157	210.945	1.00375	
translation initiation factor if-2. [source:swissprot;acc:o60841]	1691	217.263	214.315	1.01376	
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	1109	218.098	212.209	1.02775	
translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	783	224.385	235.131	1.04789	
translin. [source:swissprot;acc:q15631]	782	224.385	235.131	1.04789	
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [source:swissprot;acc:p51571]	2698	188.435	188.31	1.00066	
transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [source:swissprot;acc:q9hd45]	3174	0.00001	0.00001	1	
transmembrane protein 4. [source:refseq;acc:nm_014255]	2923	0.00001	0.00001	1	
transportin-sr; importin 12. [source:refseq;acc:nm_012470]	1449	225.305	229.766	1.0198	
transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [source:swissprot;acc:p02766]	3041	0.00001	0.00001	1	
trap/mediator complex component trap25. [source:refseq;acc:nm_080651]	1409	206.102	210.42	1.02095	
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [source:swissprot;acc:o43280]	722	217.952	206.902	1.05341	
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [source:swissprot;acc:p07098]	2114	214.632	213.14	1.007	
trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [source:swissprot;acc:p22102]	843	218.521	227.796	1.04244	
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [source:swissprot;acc:q9nvh6]	1542	213.546	209.965	1.01706	
trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	747	250.465	238.38	1.0507	
trinucleotide repeat containing 6; edie; gw182 autoantigen. [source:refseq;acc:nm_014494]	3159	0.00001	0.00001	1	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/