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 3658 to 3707 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
229 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Measured Subtracted 0 1225.08 1079.38 145.7
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted Divided 1 137.446 120.823 1.13758
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Squared 42411.6 55802.1 1.31573
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Measured 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Rooted Subtracted 95.0526 85.3206 9.732
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Ranked Divided 0 10899.4 9878.1 1.10339
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Measured Subtracted 1 10434.4 11846.2 1411.8
230 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Squared 45987 56777.1 10790.1
casein kinase i alpha s-like. [refseq;acc:nm_145203] Rooted Divided 0 35.3509 31.4916 1.12255
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Subtracted 22.2195 19.7836 2.4359
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Ranked Divided 1 239.35 267.915 1.11934
histone h2b.d (h2b/d). [swissprot;acc:q99877] Squared Subtracted 0 7089.47 7293.03 203.56
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Ranked 15147.2 14091.9 1055.3
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Measured 1 9649.61 11053.5 1403.89
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Rooted Subtracted 95.0526 85.3206 9.732
necdin. [swissprot;acc:q99608] Divided 137.446 120.823 1.13758
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Ranked Subtracted 242.694 267.017 24.323
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Squared Divided 0 82802.3 111762 1.34975
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 1 42411.6 55802.1 1.31573
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Measured Subtracted 0 1225.08 1079.38 145.7
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Ranked Divided 12364.7 11207.7 1.10323
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Measured 1498.17 1718.6 1.14713
231 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked Subtracted 12447.6 11392.6 1055
60s ribosomal protein l9. [swissprot;acc:p32969] Rooted 26.3707 28.8011 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 2017.91 1759.22 1.14705
espin. [refseq;acc:nm_031475] Subtracted 1225.07 1079.38 145.69
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Squared 1 45960.8 56749.6 10788.8
histone h2b. [refseq;acc:nm_175055] 0 7090.75 7294.29 203.54
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Rooted Divided 25.0015 28.0435 1.12167
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Ranked 1 239.336 267.881 1.11927
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Rooted 137.446 120.823 1.13758
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Measured 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted Subtracted 95.0526 85.3206 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 226.411 202.088 24.323
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared Divided 0 1914.2 1419.67 1.34834
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Measured Subtracted 1 9649.61 11053.5 1403.89
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Ranked Divided 0 12364.8 11207.9 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 42411.6 55802.1 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 0.108639 0.145878 1.34278
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Ranked Subtracted 12448.9 11393.9 1055
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Measured Divided 1663.73 1906.28 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 15.8745 18.303 2.4285
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Ranked 1 226.401 202.094 24.307
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Squared 41502.9 30836.8 10666.1
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Measured Divided 9035 7279.6 1.24114
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Rooted 0 15.6205 13.9284 1.12149
histone h2b.s (h2b/s). [swissprot;acc:p57053] Squared Subtracted 7090.47 7294.01 203.54
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Measured 2075.64 2220.68 145.04
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Ranked Divided 12394.7 11240.2 1.10271

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/