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 13364 to 13413 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1169 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Rooted Subtracted 59.8204 62.7321 2.9117
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Squared 29823.4 32961.5 3138.1
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Divided 19625.9 22341.9 1.13839
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Ranked Subtracted 219.023 213.606 5.417
zinc finger protein 207. [swissprot;acc:o43670] Measured Divided 5470.44 5949.49 1.08757
1170 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Ranked 219.399 213.784 1.02626
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Squared Subtracted 21068.2 24205.2 3137
fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Rooted Divided 62.8958 65.8878 1.04757
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Squared 20923.6 23813.2 1.1381
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Measured Subtracted 5494.73 6001.08 506.35
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Ranked 219.022 213.607 5.415
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Rooted 58.6583 61.5643 2.906
ubiquitin-like protein smt3a. [swissprot;acc:p55854] Measured Divided 5826.34 6335.98 1.08747
1171 40s ribosomal protein s28. [swissprot;acc:p25112] Rooted 70.4215 73.7627 1.04745
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Ranked 219.399 213.784 1.02626
microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Squared 20923.6 23813.2 1.1381
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Rooted Subtracted 58.6583 61.5643 2.906
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Measured 4986.58 5492.51 505.93
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Squared 21068.2 24205.2 3137
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Ranked 173.475 178.889 5.414
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Measured Divided 5826.29 6335.93 1.08747
1172 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 5826.32 6335.95
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Subtracted 5890.62 6396.53 505.91
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Ranked 173.475 178.889 5.414
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Rooted Divided 63.4397 66.4483 1.04742
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Squared Subtracted 43485.2 40358.3 3126.9
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Ranked Divided 219.375 213.767 1.02623
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Squared 20923.6 23813.2 1.1381
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Rooted Subtracted 58.6583 61.5643 2.906
1173 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Measured 5892.05 6397.28 505.23
candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Ranked Divided 229.243 235.246 1.02619
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Measured 5799.35 6305.95 1.08735
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Squared 20923.6 23813.2 1.1381
coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Ranked Subtracted 171.341 176.746 5.405
cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Rooted Divided 60.9172 63.8009 1.04734
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Subtracted 59.8698 62.7727 2.9029
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Squared 21394.9 24518.9 3124
1174 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] Rooted Divided 60.9172 63.8009 1.04734
bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Squared 20923.6 23813.2 1.1381
cda11 protein. [refseq;acc:nm_032026] Measured 5874.11 6387.23 1.08735
chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Ranked Subtracted 214.364 219.759 5.395
coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] Divided 187.964 192.849 1.02599
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Measured Subtracted 4088.63 4593.43 504.8
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Squared 24948.9 28072.6 3123.7
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Rooted 61.2655 64.1634 2.8979
1175 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Measured Divided 5799.35 6305.95 1.08735
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Subtracted 4088.63 4593.43 504.8
importin 8; ran-binding protein 8. [refseq;acc:nm_006390] Squared 24948.9 28072.6 3123.7
kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Ranked 214.364 219.759 5.395
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Rooted Divided 61.2655 64.1634 1.0473

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/