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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Gene Rank description Value Type Interaction Map Network Comparison Type Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
green
red
network_comparison
231 60s ribosomal protein l9. [swissprot;acc:p32969] Rooted Subtracted 0 28.8011 26.3707 2.4304
alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Measured Divided 1759.22 2017.91 1.14705
espin. [refseq;acc:nm_031475] Subtracted 1079.38 1225.07 145.69
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Squared 1 56749.6 45960.8 10788.8
histone h2b. [refseq;acc:nm_175055] 0 7294.29 7090.75 203.54
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Rooted Divided 28.0435 25.0015 1.12167
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Ranked 1 267.881 239.336 1.11927
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Rooted 120.823 137.446 1.13758
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Measured 7279.6 9035 1.24114
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted Subtracted 85.3206 95.0526 9.732
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Ranked 202.088 226.411 24.323
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared Divided 0 1419.67 1914.2 1.34834
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Measured Subtracted 1 11053.5 9649.61 1403.89
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Ranked Divided 0 11207.9 12364.8 1.10322
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Squared 1 55802.1 42411.6 1.31573
232 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 0 0.145878 0.108639 1.34278
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Ranked Subtracted 11393.9 12448.9 1055
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Measured Divided 1906.28 1663.73 1.14579
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Rooted Subtracted 18.303 15.8745 2.4285
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Ranked 1 202.094 226.401 24.307
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Squared 30836.8 41502.9 10666.1
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Measured Divided 7279.6 9035 1.24114
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Rooted 0 13.9284 15.6205 1.12149
histone h2b.s (h2b/s). [swissprot;acc:p57053] Squared Subtracted 7294.01 7090.47 203.54
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Measured 2220.68 2075.64 145.04
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Ranked Divided 11240.2 12394.7 1.10271
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Rooted 1 120.823 137.446 1.13758
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Subtracted 85.3206 95.0526 9.732
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Squared Divided 55802.1 42411.6 1.31573
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Ranked 267.879 239.336 1.11926
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Measured Subtracted 11053.5 9649.61 1403.89
233 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Ranked Divided 0 10560 9586.97 1.1015
60s ribosomal protein l15. [swissprot;acc:p39030] Rooted Subtracted 17.0546 19.482 2.4274
60s ribosomal protein l7. [swissprot;acc:p18124] Ranked 1 259.984 235.727 24.257
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Measured 0 6303 6158 145
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Squared Divided 3966.41 5294.83 1.33492
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Subtracted 1 30836.8 41502.9 10666.1
histone h2b.e (h2b/e). [swissprot;acc:q99879] 0 7294.33 7090.8 203.53
huntingtin interacting protein c. [refseq;acc:nm_012272] Rooted Divided 19.7536 22.1446 1.12104
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Ranked 1 267.842 239.32 1.11918
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Measured 0 399.534 348.823 1.14538
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Squared 1 55802.1 42411.6 1.31573
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Rooted 120.823 137.446 1.13758
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted 85.3206 95.0526 9.732
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Measured Divided 7279.6 9035 1.24114
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Subtracted 11053.5 9649.61 1403.89
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Ranked 0 9320.25 10367 1046.75
234 40s ribosomal protein s23. [swissprot;acc:p39028] 1 268.195 243.944 24.251
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Divided 256.835 287.41 1.11905
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Rooted 0 17.8885 16.0012 1.11795

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/