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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1329 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Subtracted 7497.96 7967.09 469.13
1330 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Divided 5779.83 6244.56 1.08041
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Subtracted 3996.81 4465.61 468.8
1331 glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] 6089.43 6558.02 468.59
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Divided 5799.29 6265.2 1.08034
1332 my016 protein. [sptrembl;acc:q9h3k6] 4775.25 5158.86 1.08033
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Subtracted 5315.76 5782.63 466.87
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] Divided 5803.95 6269.44 1.0802
alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] Subtracted 5887.82 6354.58 466.76
1334 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 5420.87 5887.53 466.66
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Divided 5804.75 6270.15 1.08018
1335 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] 10430.3 9656.4 1.08014
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] Subtracted 5887.86 6354.51 466.65
1336 dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] 6354.5 466.64
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] Divided 6140.18 6632.24 1.08014
1337 elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Subtracted 5887.86 6354.5 466.64
gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] Divided 4935.58 5329.93 1.0799
1338 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] Subtracted 5887.88 6354.47 466.59
megf6 (fragment). [sptrembl;acc:o75095] Divided 5980.41 6457.51 1.07978
1339 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 5988.06 6464.94 1.07964
alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Subtracted 5887.89 6354.45 466.56
1340 proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] Divided 5979.07 6453.53 1.07935
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Subtracted 5799.29 6265.2 465.91
1341 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] 5803.95 6269.44 465.49
alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] Divided 5887.82 6354.58 1.07928
1342 dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] 5887.86 6354.51 1.07926
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Subtracted 7514.8 7980.22 465.42
1343 dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] Divided 5887.86 6354.5 1.07925
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Subtracted 5804.75 6270.15 465.4
1344 elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Divided 5887.86 6354.5 1.07925
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Subtracted 6360.13 6825.36 465.23
1345 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] Divided 5887.88 6354.47 1.07925
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Subtracted 4079.81 4545.01 465.2
1346 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Divided 5887.89 6354.45 1.07924
sestrin 3. [swissprot;acc:p58005] Subtracted 5655.85 6120.65 464.8
1347 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Divided 6153.36 6640.77 1.07921
sestrin 2 (hi95). [swissprot;acc:p58004] Subtracted 5655.85 6120.65 464.8
1348 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 6120.64 464.79
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Divided 6153.36 6640.77 1.07921
1349 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Subtracted 5655.85 6120.64 464.79
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Divided 6153.36 6640.77 1.07921
1350 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Subtracted 5655.85 6120.64 464.79
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Divided 6783.78 7320.39 1.0791
1351 dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] 6105.23 6587.88 1.07906
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Subtracted 5655.85 6120.64 464.79
1352 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]
dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] Divided 6104.11 6586.48 1.07902
1353 cyclin c. [swissprot;acc:p24863] 6200.93 6690.57 1.07896
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Subtracted 5655.85 6120.64 464.79
1354 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Divided 6036.22 6512.64 1.07893

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/