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 5858 to 5907 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1465 glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Rooted 65.2132 67.7352 1.03867
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Ranked 217.351 213.18 1.01957
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Squared 15697.5 17531.8 1.11685
1466 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 15707.2 17540.4 1.11671
glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Rooted 65.2132 67.7352 1.03867
proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] Measured 6523.17 7019.44 1.07608
reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Ranked 207.022 211.073 1.01957
1467 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 228.513 232.983 1.01956
p47 protein isoform a. [refseq;acc:nm_016143] Measured 6444.4 6932.39 1.07572
pbk1 protein. [sptrembl;acc:o76021] Squared 15711.4 17543.5 1.11661
receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Rooted 60.3015 62.6331 1.03867
1468 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Ranked 212.001 207.937 1.01954
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Rooted 60.3015 62.6328 1.03866
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Measured 5473.09 5887.45 1.07571
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Squared 29588 33034.4 1.11648
1469 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] Measured 5473.09 5887.45 1.07571
receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] Rooted 60.3015 62.6328 1.03866
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Ranked 207.013 211.05 1.0195
wd-repeat protein bing4. [swissprot;acc:o15213] Squared 15718 17545.7 1.11628
1470 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Rooted 64.2947 66.7681 1.03847
glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] Ranked 221.412 217.199 1.0194
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Measured 5473.09 5887.45 1.07571
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] Squared 24169.9 26980.2 1.11627
1471 40s ribosomal protein s8. [swissprot;acc:p09058] Measured 5659.45 6087.55 1.07564
immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] Squared 24169.9 26980.2 1.11627
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Ranked 221.412 217.199 1.0194
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Rooted 56.8024 54.6981 1.03847
1472 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] Measured 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
eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] Squared 23399.4 26118 1.11618
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] Ranked 221.412 217.199 1.0194
1473 calmegin precursor. [swissprot;acc:o14967] Measured 5910.06 6355.08 1.0753
glutamyl trna synthetase. [sptrembl;acc:o14563] Ranked 221.412 217.199 1.0194
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Squared 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
1474 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Squared 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
1475 bystin. [swissprot;acc:q13895] Squared 16837.1 18786.1 1.11576
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Ranked 181.882 178.438 1.0193
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Rooted 63.0132 65.421 1.03821
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Measured 5910.06 6355.08 1.0753
1476 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] Squared 26860.7 29969 1.11572
limkain beta 2. [refseq;acc:nm_025140] Rooted 61.9899 64.3578 1.0382
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Ranked 218.591 214.457 1.01928
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Measured 5910.06 6355.08 1.0753
1477 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Squared 26860.7 29969 1.11572
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Measured 3687.37 3429.37 1.07523
proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Rooted 63.207 65.62 1.03818

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/