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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3808 to 3857 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
238 uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Squared Divided 0 5219.15 3979.89 1.31138
239 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Subtracted 6970.13 6794.39 175.74
adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 1 36563.7 46971.1 10407.4
alpha crystallin a chain. [swissprot;acc:p02489] Rooted 0 6.22183 8.63381 2.41198
carboxypeptidase b precursor. [refseq;acc:nm_020361] Measured Divided 1 7711.38 6265.8 1.23071
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Squared 0 43393.5 56658.6 1.30569
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Ranked Subtracted 1 243.817 267.962 24.145
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Divided 227.357 254.15 1.11785
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Measured 0 382.142 434.366 1.13666
keratin associated protein 1.5. [refseq;acc:nm_031957] Ranked Subtracted 10551.6 11573.7 1022.1
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Measured 11170.7 11305 134.3
mad protein (max dimerizer). [swissprot;acc:q05195] Rooted 1 55.646 65.1534 9.5074
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 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
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Ranked 0 8907.41 9795.36 1.09969
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Measured Subtracted 1 9649.61 11053.5 1403.89
p28 ing5. [refseq;acc:nm_032329] Rooted Divided 0 32.711 36.4589 1.11458
240 40s ribosomal protein s28. [swissprot;acc:p25112] Squared Subtracted 1054.58 879.603 174.977
androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Ranked Divided 1 227.357 254.15 1.11785
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] Subtracted 252.39 228.297 24.093
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] Rooted Divided 0 19.303 21.5023 1.11394
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Ranked Subtracted 10551.6 11573.7 1022.1
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Rooted 14.1274 16.5305 2.4031
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured Divided 1 7711.36 6265.79 1.23071
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Rooted Subtracted 55.6486 65.1478 9.4992
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 137.446 120.823 1.13758
methyltransferase like 2. [refseq;acc:nm_018396] Ranked 0 17946 16326 1.09923
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 1 42411.6 55802.1 1.31573
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Measured Subtracted 9649.61 11053.5 1403.89
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Divided 0 1475.83 1676.18 1.13575
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Squared 7071.05 5421.2 1.30433
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured Subtracted 903.967 771.309 132.658
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Squared 1 58831 48584.2 10246.8
241 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Divided 0 4734.34 6172.1 1.30369
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Subtracted 2967.63 3141.67 174.04
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Ranked Divided 1 227.357 254.15 1.11785
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Rooted Subtracted 0 23.9664 21.5733 2.3931
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Ranked 1 241.892 265.96 24.068
fos-related antigen 2. [swissprot;acc:p15408] Rooted Divided 0 44.3292 39.9005 1.11099
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Measured Subtracted 3614.24 3481.87 132.37
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Ranked 10551.6 11573.7 1022.1
keratin associated protein 9.2. [refseq;acc:nm_031961] Measured Divided 1225.47 1079.01 1.13574
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Rooted Subtracted 1 55.6495 65.1458 9.4963
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Divided 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] 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
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Ranked 0 14003.7 12743.3 1.09891
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Squared Subtracted 1 58831 48584.2 10246.8
242 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked Divided 0 15260.6 13895.8 1.09822

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/