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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description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5858 to 5907 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
description
Rank
Network Comparison Type
red
green
network_comparison
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] 2419 Divided 218.2 218.984 1.00359
translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] 2027 Subtracted 220.787 222.634 1.847
2049 Divided 1.00837
translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] 1831 Subtracted 221.725 224.133 2.408
1866 Divided 1.01086
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] 1822 Subtracted 222.215 224.637 2.422
1854 Divided 1.0109
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] 1823 Subtracted 2.422
1857 Divided 1.0109
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] 2397 210.157 210.945 1.00375
2400 Subtracted 0.788
translation initiation factor if-2. [swissprot;acc:o60841] 1685 217.263 214.315 2.948
1691 Divided 1.01376
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] 1077 Subtracted 218.098 212.209 5.889
1109 Divided 1.02775
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] 733 Subtracted 224.385 235.131 10.746
783 Divided 1.04789
translin. [swissprot;acc:q15631] 732 Subtracted 10.746
782 Divided 1.04789
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 2698 188.435 188.31 1.00066
2706 Subtracted 0.125
transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45] 3174 Divided 0.00001 0.00001 1
Subtracted 0 0 0
transmembrane protein 4. [refseq;acc:nm_014255] 2923 Divided 0.00001 0.00001 1
Subtracted 0 0 0
transportin-sr; importin 12. [refseq;acc:nm_012470] 1386 225.305 229.766 4.461
1449 Divided 1.0198
transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766] 3041 0.00001 0.00001 1
Subtracted 0 0 0
trap/mediator complex component trap25. [refseq;acc:nm_080651] 1409 Divided 206.102 210.42 1.02095
Subtracted 4.318
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] 720 217.952 206.902 11.05
722 Divided 1.05341
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] 2114 214.632 213.14 1.007
2129 Subtracted 1.492
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)]. [swissprot;acc:p22102] 807 218.521 227.796 9.275
843 Divided 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). [swissprot;acc:q9nvh6] 1542 213.546 209.965 1.01706
1571 Subtracted 3.581
trinucleotide repeat containing 15. [refseq;acc:nm_015575] 667 250.465 238.38 12.085
747 Divided 1.0507
trinucleotide repeat containing 6; edie; gw182 autoantigen. [refseq;acc:nm_014494] 3159 0.00001 0.00001 1
Subtracted 0 0 0
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] 436 231.496 248.048 16.552
499 Divided 1.0715
tripartite motif protein 2. [swissprot;acc:q9c040] 2268 202.312 203.437 1.00556
2281 Subtracted 1.125
tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382] 2233 Divided 202.414 203.691 1.00631
2241 Subtracted 1.277
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] 936 217.253 209.827 7.426

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.
- http://analysis.yellowcouch.org/