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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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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX
Showing element 3063 to 3112 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
3063\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
MRPS30\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [source:swissprot;acc:q9np92]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3064\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
C7\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
complement component c7 precursor. [source:swissprot;acc:p10643]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3065\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
WISP3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [source:refseq;acc:nm\_003880]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3066\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
VEGFA\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [source:swissprot;acc:p15692]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3067\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
retinoic acid receptor rxr-beta. [source:swissprot;acc:p28702]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3068\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
HECA\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
headcase homolog; hhdc for homolog of drosophila headcase. [source:refseq;acc:nm\_016217]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3069\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
BMP5\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
bone morphogenetic protein 5 precursor (bmp-5). [source:swissprot;acc:p22003]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3070\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
MDGA1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [source:refseq;acc:nm\_153487]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3071\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
STK38\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
serine/threonine kinase 38; serine threonine protein kinase. [source:refseq;acc:nm\_007271]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3072\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PAK1IP1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
pak1 interacting protein 1; pak1-interacting protein; pak/plc-interacting protein 1. [source:refseq;acc:nm\_017906]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3073\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
RWDD1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm\_015952]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3074\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
NT5DC3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
tu12b1-ty protein. [source:refseq;acc:nm\_016575]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3075\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
USP5\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [source:swissprot;acc:p45974]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3076\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
placental protein 11 precursor (ec 3.4.21.-) (pp11). [source:swissprot;acc:p21128]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3077\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
H2AFJ\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
h2a histone family, member j isoform 1. [source:refseq;acc:nm\_018267]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3078\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CREBL2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
camp responsive element binding protein-like 2. [source:refseq;acc:nm\_001310]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3079\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CYP27B1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3080\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3081\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PTPMT1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [source:swissprot;acc:o75489]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3082\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CRYAB\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [source:swissprot;acc:p02511]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3083\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
GLRB\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
glycine receptor beta chain precursor (glycine receptor 58 kda subunit). [source:swissprot;acc:p48167]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3084\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
MAP2K1IP1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [source:swissprot;acc:q9uha4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3085\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
UGT2B10\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [source:swissprot;acc:p36537]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3086\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [source:swissprot;acc:p54855]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3087\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ALDOC\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [source:swissprot;acc:p09972]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3088\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
YWHAE\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [source:swissprot;acc:p42655]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3089\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PRKAR1A\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [source:swissprot;acc:p10644]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3090\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
EZH1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
enhancer of zeste homolog 1 (enx-2). [source:swissprot;acc:q92800]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3091\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
MLX\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
transcription factor-like protein 4 (max-like bhlhzip protein) (bigmax protein) (mlx). [source:swissprot;acc:q9uh92]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3092\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
DRG2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
developmentally regulated gtp-binding protein 2 (drg 2). [source:swissprot;acc:p55039]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3093\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ptd016 protein. [source:refseq;acc:nm\_016125]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3094\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
UBE2S\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [source:swissprot;acc:q16763]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3095\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
C10orf137\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
erythroid differentiation-related factor 1. [source:refseq;acc:nm\_015608]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3096\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
NPM3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
nucleoplasmin 3. [source:swissprot;acc:o75607]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3097\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SEC23IP\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
sec23-interacting protein p125; phospholipase. [source:refseq;acc:nm\_007190]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3098\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
EZH2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
enhancer of zeste homolog 2 (enx-1). [source:swissprot;acc:q15910]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3099\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CAV1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
caveolin-1. [source:swissprot;acc:q03135]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3100\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [source:refseq;acc:nm\_172341]\vspace{3pt}}\\\cline{1-1}\cline{3-3}
\parbox{\wcA}{\vspace{3pt}\noindent
3101\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
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/