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 19220 to 19269 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2403 dymeclin. [refseq;acc:nm_017653] Squared Divided 26996.7 28788.6 1.06637
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Ranked Subtracted 218.2 218.984 0.784
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Squared 15953.2 17274.4 1321.2
mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Rooted Divided 60.8344 61.7685 1.01535
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Measured Subtracted 5978.83 6166.89 188.06
2404 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Squared 13245.8 14566.6 1320.8
60s ribosomal protein l3-like. [swissprot;acc:q92901] Measured 3617.81 3430.31 187.5
acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] Ranked Divided 193.389 194.105 1.0037
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Measured 5078.5 5275.76 1.03884
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Rooted Subtracted 58.6893 57.7518 0.9375
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] Ranked 218.2 218.984 0.784
sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] Squared Divided 26996.7 28788.6 1.06637
transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] Rooted 57.6124 58.4763 1.015
2405 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Subtracted 58.6893 57.7518 0.9375
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Squared 15945.8 17266.4 1320.6
hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] Measured 4457.6 4642.72 185.12
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Rooted Divided 60.6732 61.5778 1.01491
lats homolog 1. [refseq;acc:nm_004690] Squared 26996.7 28788.6 1.06637
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Measured 5078.5 5275.76 1.03884
thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] Ranked 221.677 222.489 1.00366
upf0183 protein. [swissprot;acc:q9bsu1] Subtracted 218.2 218.984 0.784
2406 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Squared 13244.1 14564.4 1320.3
antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008] Ranked 218.2 218.984 0.784
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Measured Divided 5078.5 5275.76 1.03884
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Rooted 58.7808 57.9198 1.01487
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Measured Subtracted 3544.03 3359.43 184.6
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Rooted 58.6893 57.7518 0.9375
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Squared Divided 26996.7 28788.6 1.06637
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Ranked 182.563 183.232 1.00366
2407 40s ribosomal protein s16. [swissprot;acc:p17008] Squared Subtracted 13244.1 14564.4 1320.3
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Measured 3544.03 3359.43 184.6
microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Rooted Divided 58.7808 57.9198 1.01487
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782] Squared 26996.7 28788.6 1.06637
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Measured 5078.5 5275.76 1.03884
proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Ranked 214.234 213.456 1.00364
serpin b11. [swissprot;acc:q96p15] Rooted Subtracted 58.6893 57.7518 0.9375
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Ranked 218.2 218.984 0.784
2408 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Measured 5454.62 5637.88 183.26
dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125] Squared Divided 26996.7 28788.6 1.06637
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Ranked 194.407 193.706 1.00362
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Rooted Subtracted 58.6893 57.7518 0.9375
rad50-interacting protein 1. [refseq;acc:nm_021930] Squared 48.0356 1357.07 1309.03
serpin b11. [swissprot;acc:q96p15] Measured Divided 5078.5 5275.76 1.03884
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Ranked Subtracted 218.2 218.984 0.784
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Rooted Divided 58.7808 57.9198 1.01487
2409 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Measured Subtracted 4857.03 5039.78 182.75
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Rooted Divided 58.7808 57.9198 1.01487
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Subtracted 58.6893 57.7518 0.9375
lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Ranked Divided 194.407 193.706 1.00362
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Subtracted 218.2 218.984 0.784

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/