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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 11764 to 11813 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1471 immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] Squared Divided 24169.9 26980.2 1.11627
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Ranked Subtracted 171.231 167.177 4.054
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Divided 221.412 217.199 1.0194
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Rooted 56.8024 54.6981 1.03847
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Subtracted 64.181 66.575 2.394
1472 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] Measured Divided 5984.47 6435.42 1.07535
adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] Rooted 64.2954 66.7683 1.03846
alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] Squared Subtracted 27296.6 29989.9 2693.3
eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] Divided 23399.4 26118 1.11618
fetal brain protein 239 (239fb). [swissprot;acc:q15777] Measured Subtracted 4757.46 5198.91 441.45
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] Ranked Divided 221.412 217.199 1.0194
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Subtracted 171.231 167.177 4.054
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] Rooted 64.181 66.575 2.394
1473 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Squared 27296.5 29989.7 2693.2
calmegin precursor. [swissprot;acc:o14967] Measured Divided 5910.06 6355.08 1.0753
glutamyl trna synthetase. [sptrembl;acc:o14563] Ranked 221.412 217.199 1.0194
homeobox protein dlx-3. [swissprot;acc:o60479] Measured Subtracted 4757.46 5198.91 441.45
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Ranked 171.231 167.177 4.054
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Squared Divided 15766.9 17597.5 1.1161
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Rooted 80.6874 83.7879 1.03843
rest corepressor. [refseq;acc:nm_015156] Subtracted 64.181 66.575 2.394
1474 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Measured 4757.46 5198.91 441.45
apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Squared Divided 15792.5 17625.2 1.11605
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Measured 5910.06 6355.08 1.0753
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Ranked 218.582 214.427 1.01938
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Rooted 60.3017 62.6158 1.03838
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Squared Subtracted 26908.6 29598.5 2689.9
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Ranked 171.231 167.177 4.054
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Rooted 64.4036 66.795 2.3914
1475 bystin. [swissprot;acc:q13895] Squared Divided 16837.1 18786.1 1.11576
elks protein. [refseq;acc:nm_015064] Subtracted 26908.6 29598.5 2689.9
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Rooted 64.4036 66.795 2.3914
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Ranked Divided 181.882 178.438 1.0193
mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Measured Subtracted 4757.46 5198.91 441.45
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Rooted Divided 63.0132 65.421 1.03821
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Measured 5910.06 6355.08 1.0753
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Ranked Subtracted 171.231 167.177 4.054
1476 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] Squared Divided 26860.7 29969 1.11572
60s ribosomal protein l39. [swissprot;acc:p02404] Subtracted 18854.4 21540.4 2686
limkain beta 2. [refseq;acc:nm_025140] Rooted Divided 61.9899 64.3578 1.0382
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Subtracted 64.4036 66.795 2.3914
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Ranked Divided 218.591 214.457 1.01928
reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Subtracted 207.022 211.073 4.051
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Measured Divided 5910.06 6355.08 1.0753
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Subtracted 6078.43 6519.6 441.17
1477 60s ribosomal protein l18a. [swissprot;acc:q02543] Squared 18854.4 21540.4 2686
adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Divided 26860.7 29969 1.11572
colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Rooted Subtracted 66.302 68.6843 2.3823
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] Measured 6176.82 6617.91 441.09
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Divided 3687.37 3429.37 1.07523

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/