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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1925 to 1974 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
241 mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Measured Subtracted 9649.61 11053.5 1403.89
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared Divided 42411.6 55802.1 1.31573
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Measured 7711.31 6265.76 1.23071
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Squared Subtracted 58831 48584.2 10246.8
242 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Ranked 241.892 265.959 24.067
j domain containing protein 1. [swissprot;acc:q9ukb3] Divided 227.357 254.15 1.11785
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Squared Subtracted 35991.8 46002.9 10011.1
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Rooted 55.65 65.1448 9.4948
max protein. [swissprot;acc:p25912] Measured Divided 4640.26 5704.87 1.22943
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Rooted 137.446 120.823 1.13758
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Squared 42411.6 55802.1 1.31573
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Measured Subtracted 9649.61 11053.5 1403.89
243 60s ribosomal protein l23a. [swissprot;acc:p29316] Ranked 241.884 265.945 24.061
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Squared 51805.2 41916.4 9888.8
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Measured Divided 4246.95 5208.98 1.22652
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Subtracted 9649.61 11053.5 1403.89
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Rooted 63.1192 72.584 9.4648
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Ranked Divided 227.357 254.15 1.11785
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Squared 42411.6 55802.1 1.31573
trophinin. [swissprot;acc:q12816] Rooted 137.446 120.823 1.13758
244 60s ribosomal protein l5. [swissprot;acc:p46777] Ranked Subtracted 241.899 265.924 24.025
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Divided 227.357 254.15 1.11785
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared 14728.8 19330.8 1.31245
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Rooted 146.94 167.046 1.13683
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Subtracted 27.9136 37.2872 9.3736
scratch; scratch 1. [refseq;acc:nm_031309] Squared 40388.9 49827.5 9438.6
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Measured 9649.61 11053.5 1403.89
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 4250.14 5211.25 1.22614
245 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Squared 8875.01 6768.05 1.31131
60s ribosomal protein l19. [swissprot;acc:p14118] Ranked Subtracted 240.73 264.729 23.999
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Rooted 27.9136 37.2872 9.3736
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Squared 40315.7 49716.4 9400.7
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured Divided 4251.65 5212.33 1.22595
methyltransferase like 2. [refseq;acc:nm_018396] Subtracted 13241.4 11864 1377.4
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Rooted Divided 146.94 167.046 1.13683
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Ranked 226.109 202.333 1.11751
246 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 243.583 267.528 23.945
cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Measured 13241.4 11864 1377.4
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Rooted 27.9136 37.2872 9.3736
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Ranked Divided 237.312 212.363 1.11748
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Squared 8875.01 6768.05 1.31131
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Subtracted 54726.7 45358.5 9368.2
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured Divided 4252.66 5213.05 1.22583
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Rooted 146.94 167.046 1.13683
247 60s ribosomal protein l12. [swissprot;acc:p30050] Ranked Subtracted 243.583 267.527 23.944
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Measured 13241.4 11864 1377.4
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Squared Divided 8875.01 6768.05 1.31131
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Rooted Subtracted 27.9136 37.2872 9.3736
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Squared 33982.3 43159.1 9176.8
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Rooted Divided 47.3621 53.8355 1.13668

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/