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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Network Comparison Type description Value Type red Interaction Map green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1900 to 1949 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
Value Type
red
green
network_comparison
238 Divided rd protein. [swissprot;acc:p18615] Ranked 227.357 254.15 1.11785
Subtracted golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Squared 42566.2 52985.3 10419.1
metastasis-associated protein mta1. [swissprot;acc:q13330] Ranked 252.512 228.356 24.156
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Rooted 56.3709 65.8949 9.524
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Measured 9649.61 11053.5 1403.89
239 Divided carboxypeptidase b precursor. [refseq;acc:nm_020361] 7711.38 6265.8 1.23071
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Ranked 227.357 254.15 1.11785
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Rooted 137.446 120.823 1.13758
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Squared 42411.6 55802.1 1.31573
Subtracted adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 36563.7 46971.1 10407.4
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Ranked 243.817 267.962 24.145
mad protein (max dimerizer). [swissprot;acc:q05195] Rooted 55.646 65.1534 9.5074
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Measured 9649.61 11053.5 1403.89
240 Divided androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Ranked 227.357 254.15 1.11785
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured 7711.36 6265.79 1.23071
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Rooted 137.446 120.823 1.13758
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] Squared 42411.6 55802.1 1.31573
Subtracted chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Ranked 252.39 228.297 24.093
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Rooted 55.6486 65.1478 9.4992
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Measured 9649.61 11053.5 1403.89
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Squared 58831 48584.2 10246.8
241 Divided atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Ranked 227.357 254.15 1.11785
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Rooted 137.446 120.823 1.13758
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared 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
Subtracted epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Ranked 241.892 265.96 24.068
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Rooted 55.6495 65.1458 9.4963
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 9649.61 11053.5 1403.89
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Squared 58831 48584.2 10246.8
242 Divided j domain containing protein 1. [swissprot;acc:q9ukb3] Ranked 227.357 254.15 1.11785
max protein. [swissprot;acc:p25912] Measured 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
Subtracted 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
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Squared 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
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Measured 9649.61 11053.5 1403.89
243 Divided homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 4246.95 5208.98 1.22652
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Ranked 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
Subtracted 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
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Measured 9649.61 11053.5 1403.89
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Rooted 63.1192 72.584 9.4648
244 Divided ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Ranked 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
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Measured 4250.14 5211.25 1.22614
Subtracted 60s ribosomal protein l5. [swissprot;acc:p46777] Ranked 241.899 265.924 24.025

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/