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 5758 to 5807 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
720 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Measured Divided 6593.17 7364.55 1.117
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Ranked Subtracted 217.952 206.902 11.05
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Squared Divided 25911.5 30281.9 1.16867
721 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Measured Subtracted 5874.74 6533.34 658.6
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Ranked Divided 214.765 203.8 1.0538
Subtracted 10.965
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Rooted Divided 60.8463 65.123 1.07029
surfeit locus protein 5. [swissprot;acc:q15528] Subtracted 50.4595 46.0413 4.4182
syntaxin 7. [swissprot;acc:o15400] Measured Divided 5580.97 6233.52 1.11692
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Squared 25911.7 30282.1 1.16867
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Subtracted 25842.1 30093.4 4251.3
722 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Rooted Divided 58.4551 62.5601 1.07022
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Squared 25911.7 30282.1 1.16867
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Measured 8061.05 9002.33 1.11677
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Ranked Subtracted 244.447 233.508 10.939
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Squared 18995.7 23245.6 4249.9
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Ranked Divided 217.952 206.902 1.05341
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Measured Subtracted 5874.63 6533.23 658.6
zinc finger protein 291. [swissprot;acc:q9by12] Rooted 50.4595 46.0413 4.4182
723 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Squared Divided 25911.5 30281.9 1.16867
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Rooted 51.7007 48.3103 1.07018
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Measured Subtracted 5874.76 6533.36 658.6
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Divided 8056.09 8996.46 1.11673
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Ranked 244.842 232.577 1.05274
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Rooted Subtracted 50.4595 46.0413 4.4182
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Squared 18995.7 23244.9 4249.2
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] Ranked 244.447 233.508 10.939
724 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Divided 244.842 232.577 1.05274
down-regulated in metastasis. [refseq;acc:nm_014503] Subtracted 244.447 233.508 10.939
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Squared Divided 25911.7 30282.1 1.16867
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Measured 5384.41 6012.82 1.11671
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Squared Subtracted 18995.7 23244.7 4249
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Rooted 50.4595 46.0413 4.4182
syntaxin 12. [refseq;acc:nm_177424] Divided 61.3557 65.66 1.07015
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Measured Subtracted 5874.76 6533.36 658.6
725 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted 50.4595 46.0415 4.418
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Divided 57.5045 53.7387 1.07008
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Ranked 235.296 247.673 1.0526
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Measured 5384.41 6012.82 1.11671
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Subtracted 5874.76 6533.36 658.6
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Squared 18995.6 23242.8 4247.2
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Ranked 214.679 225.568 10.889
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Squared Divided 25911.7 30282.1 1.16867
726 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Subtracted 23487.1 27726.3 4239.2
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Measured Divided 6327.86 7064.13 1.11635
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Ranked 244.495 232.419 1.05196
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Rooted Subtracted 50.1671 45.7563 4.4108
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Squared Divided 25911.7 30282.1 1.16867
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Rooted 51.4482 55.0529 1.07006
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Measured Subtracted 5874.78 6533.37 658.59

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/