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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3101 to 3150 of 3228 in total 
Value Type: Ranked
Network Comparison Type: Divided
Interaction Map: High confidence
Filtered: 1
red: 0.00001
green: 0.00001
network\_comparison: 1

\def\wcA{0.25\textwidth}
\def\wcB{0.25\textwidth}
\def\wcC{0.25\textwidth}
\begin{longtable}{|c|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
Hugo\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
description\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3101\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [source:swissprot;acc:p13284]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3102\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
C19orf56\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
protein cgi-140 (protein ptd008) (my006 protein). [source:swissprot;acc:q9y284]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3103\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
LIG1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [source:swissprot;acc:p18858]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3104\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SNORD23\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
glioma tumor suppressor candidate region gene 2 protein (p60). [source:swissprot;acc:q9nzm5]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3105\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TGFB1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
transforming growth factor beta 1 precursor (tgf-beta 1). [source:swissprot;acc:p01137]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3106\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PTOV1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [source:refseq;acc:nm\_017432]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3107\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
LYL1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
lyl-1 protein (lymphoblastic leukemia derived sequence 1). [source:swissprot;acc:p12980]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3108\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SNX16\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
sorting nexin 16. [source:swissprot;acc:p57768]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3109\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
WISP1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [source:refseq;acc:nm\_003882]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3110\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
RAB2A\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ras-related protein rab-2a. [source:swissprot;acc:p08886]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3111\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
STK3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [source:swissprot;acc:q13188]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3112\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
RAB11A\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ras-related protein rab-11a (rab-11) (24kg) (yl8). [source:swissprot;acc:p24410]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3113\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
NUTF2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [source:swissprot;acc:p13662]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3114\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TSC22D1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [source:swissprot;acc:q15714]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3115\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
STK24\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
serine/threonine protein kinase 24 (ec 2.7.1.37) (ste20-like kinase mst3) (mst-3) (mammalian ste20-like protein kinase 3). [source:swissprot;acc:q9y6e0]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3116\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CAB39L\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
mo25-like protein. [source:swissprot;acc:q9h9s4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3117\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
FNDC3A\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ba203i16.1 (hypothetical protein kiaa0970). [source:sptrembl;acc:q9h1w1]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3118\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SMS\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [source:swissprot;acc:p52788]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3119\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [source:swissprot;acc:p31150]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3120\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SCML2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
sex comb on midleg-like 2; sex comb on midleg like 2. [source:refseq;acc:nm\_006089]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3121\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
GLRA2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
glycine receptor alpha-2 chain precursor. [source:swissprot;acc:p23416]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3122\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PRPS2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ribose-phosphate pyrophosphokinase ii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase ii) (ppribp) (prs-ii). [source:swissprot;acc:p11908]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3123\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
VAPA\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [source:swissprot;acc:q9p0l0]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3124\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SAMHD1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [source:swissprot;acc:q9y3z3]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3125\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
POFUT1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [source:swissprot;acc:q9h488]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3126\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PLCB4\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [source:swissprot;acc:q15147]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3127\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SEC23B\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
protein transport protein sec23b (sec23-related protein b). [source:swissprot;acc:q15437]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3128\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
BMP7\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [source:swissprot;acc:p18075]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3129\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CSTF1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [source:swissprot;acc:q05048]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3130\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PFDN4\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
prefoldin subunit 4 (protein c-1). [source:swissprot;acc:q9nqp4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3131\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
C20orf24\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [source:swissprot;acc:q9buv8]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3132\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
R3HDML\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
r3h domain (binds single-stranded nucleic acids) containing-like. [source:refseq;acc:nm\_178491]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3133\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
IFT52\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ngd5 protein homolog (cgi-53). [source:swissprot;acc:q9y366]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3134\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
RABGGTA\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [source:swissprot;acc:q92696]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3135\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SEC23A\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
protein transport protein sec23a (sec23-related protein a). [source:swissprot;acc:q15436]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3136\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
VRK1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
vaccinia related kinase 1; vaccinia-related kinase-1. [source:refseq;acc:nm\_003384]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3137\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CDKL1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [source:swissprot;acc:q00532]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3138\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
C14orf124\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
hcdi protein. [source:refseq;acc:nm\_020195]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3139\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
BRD1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
bromodomain-containing protein 1 (br140-like protein). [source:swissprot;acc:o95696]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3140\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
MYH9\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
myosin heavy chain, nonmuscle type a (cellular myosin heavy chain, type a) (nonmuscle myosin heavy chain-a) (nmmhc-a). [source:swissprot;acc:p35579]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3141\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TTLL1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
tubulin tyrosine ligase-like protein 1. [source:swissprot;acc:o95922]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3142\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PACSIN2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
protein kinase c and casein kinase substrate in neurons protein 2. [source:swissprot;acc:q9unf0]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3143\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PICK1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [source:swissprot;acc:q9nrd5]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3144\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
HMG1L10\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
high mobility group protein 1-like 10 (hmg-1l10). [source:swissprot;acc:q9ugv6]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3145\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
UPB1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [source:swissprot;acc:q9ubr1]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3146\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
DERL3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
putative nadh oxidoreductase complex i subunit homolog. [source:sptrembl;acc:q96q80]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3147\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
HSD3B7\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [source:refseq;acc:nm\_025193]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3148\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
muts protein homolog 5. [source:swissprot;acc:o43196]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3149\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
BRPF3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
bromodomain and phd finger-containing protein 3 (fragment). [source:swissprot;acc:q9uld4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3150\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CRISP3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [source:swissprot;acc:p54108]\vspace{3pt}}\\\hline
nd{longtable}

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

 - Hugo is the HGNC identifier if it exists

 - 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/