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 Rank description Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 3630 to 3679 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
1313 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Subtracted 6815.41 6340.5 474.91
1314 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] 6453.53 5979.07 474.46
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Divided 5838.63 5401.39 1.08095
1315 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 6145.43 5685.77 1.08084
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Subtracted 6597.71 6123.75 473.96
1316 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 6812.45 6339.08 473.37
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Divided 6599.41 6105.93 1.08082
1317 orphan nuclear receptor tr2. [swissprot;acc:p13056] 6599.06 6105.69 1.0808
p10-binding protein. [refseq;acc:nm_024491] Subtracted 6067.49 5594.18 473.31
1318 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 6019.57 5546.5 473.07
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Divided 6443.07 5961.97 1.08069
1319 epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Subtracted 6157.7 5685.38 472.32
serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] Divided 6443.07 5961.97 1.08069
1320 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Subtracted 5921.77 5449.48 472.29
1321 epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] 6157.53 5685.34 472.19
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Divided 6959.21 6439.79 1.08066
1322 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
similar to trna synthetase class ii. [refseq;acc:nm_152268] Subtracted 5911.24 5439.56 471.68
1323 epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] 6156.48 5685.08 471.4
glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Divided 6959.21 6439.79 1.08066
1324 glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841]
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Subtracted 4557.68 4086.6 471.08
1325 rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]
serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] Divided 6112.02 5656.79 1.08047
1326 down-regulated in metastasis. [refseq;acc:nm_014503] Subtracted 4557.68 4086.6 471.08
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Divided 6723.54 6222.8 1.08047
1327 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] Subtracted 5793.15 5322.74 470.41
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] Divided 6111.9 5656.8 1.08045
1328 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Subtracted 5793.15 5322.74 470.41
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] Divided 6111.84 5656.81 1.08044
1329 serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] 6111.8 5656.82 1.08043
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Subtracted 7967.09 7497.96 469.13
1330 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Divided 6244.56 5779.83 1.08041
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Subtracted 4465.61 3996.81 468.8
1331 glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] 6558.02 6089.43 468.59
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Divided 6265.2 5799.29 1.08034
1332 my016 protein. [sptrembl;acc:q9h3k6] 5158.86 4775.25 1.08033
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Subtracted 5782.63 5315.76 466.87
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 6269.44 5803.95 1.0802
alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] Subtracted 6354.58 5887.82 466.76
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] 5887.53 5420.87 466.66
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 6270.15 5804.75 1.08018
1335 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] 9656.4 10430.3 1.08014
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] Subtracted 6354.51 5887.86 466.65
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 6632.24 6140.18 1.08014
1337 elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Subtracted 6354.5 5887.86 466.64
gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] Divided 5329.93 4935.58 1.0799
1338 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] Subtracted 6354.47 5887.88 466.59

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/