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 4558 to 4607 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1140 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Squared 28579.3 32606.8 1.14092
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] Rooted 61.5052 64.4938 1.04859
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Measured 5790.65 6303.93 1.08864
1141 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Ranked 218.484 212.675 1.02731
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Squared 20159.5 23000.1 1.14091
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Rooted 56.3806 59.1186 1.04856
1142 histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Squared 28578.7 32605.8 1.14091
importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Measured 5789.07 6302.01 1.0886
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Rooted 60.5003 63.437 1.04854
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] Ranked 218.484 212.675 1.02731
1143 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Squared 28551.5 32561.8 1.14046
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Measured 6281.21 6837.61 1.08858
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Ranked 218.484 212.675 1.02731
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Rooted 81.454 85.4078 1.04854
1144 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Measured 6281.21 6837.61 1.08858
dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Squared 31445.2 35847.4 1.14
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Rooted 59.8698 62.7727 1.04849
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Ranked 218.484 212.675 1.02731
1145 40s ribosomal protein s30. [swissprot;acc:q05472] Measured 5893.97 6416.07 1.08858
dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Squared 21665 24695.2 1.13987
tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] Rooted 66.1235 69.3232 1.04839
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Ranked 218.481 212.675 1.0273
1146 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Measured 6281.21 6837.61 1.08858
putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] Rooted 66.1235 69.3232 1.04839
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Squared 21665 24695.2 1.13987
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] Ranked 218.483 212.676 1.0273
1147 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] Squared 20397.1 23249.1 1.13982
cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Measured 6281.21 6837.61 1.08858
dead-box protein. [refseq;acc:nm_018665] Rooted 66.1235 69.3232 1.04839
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Ranked 208.651 203.109 1.02729
1148 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] Rooted 61.5672 64.5415 1.04831
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Squared 20397.1 23249.1 1.13982
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Measured 6281.21 6837.61 1.08858
ubiquitin. [swissprot;acc:p02248] Ranked 209.061 203.518 1.02724
1149 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Rooted 61.5672 64.5415 1.04831
bystin. [swissprot;acc:q13895] Ranked 239.505 233.185 1.0271
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Measured 6280.74 6837.01 1.08857
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] Squared 28101.6 32027.6 1.13971
1150 kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]
mstp028 protein. [refseq;acc:nm_031954] Measured 5838.87 6355.06 1.08841
sorting nexin 1. [swissprot;acc:q13596] Ranked 209.868 215.522 1.02694
translation initiation factor if-2. [swissprot;acc:o60841] Rooted 62.5721 65.592 1.04826
1151 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] Measured 5322.74 5793.15 1.08838
metaxin 1. [swissprot;acc:q13505] Ranked 199.552 204.925 1.02693
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Rooted 58.3991 61.2163 1.04824
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Squared 28101.6 32027.6 1.13971
1152 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Measured 5322.74 5793.15 1.08838
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Squared 21669.8 24695.2 1.13961
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Ranked 221.939 216.143 1.02682

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/