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 3151 to 3200 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
3151\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
MSH2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
dna mismatch repair protein msh2. [source:swissprot;acc:p43246]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3152\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
HDAC6\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
histone deacetylase 6 (hd6). [source:swissprot;acc:q9ubn7]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3153\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
LRRFIP2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
leucine rich repeat (in flii) interacting protein 2. [source:refseq;acc:nm\_006309]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3154\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
NUP50\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [source:swissprot;acc:q9ukx7]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3155\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TGFB2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
transforming growth factor beta 2 precursor (tgf-beta 2) (glioblastoma-derived t-cell suppressor factor) (g-tsf) (bsc-1 cell growth inhibitor) (polyergin) (cetermin). [source:swissprot;acc:p08112]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3156\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TEKT2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
tektin 2 (tektin-t) (testicular tektin b1-like protein). [source:swissprot;acc:q9uif3]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3157\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SCFD1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
vesicle transport-related protein isoform a; vesicle transport-related protein. [source:refseq;acc:nm\_016106]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3158\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ITGA6\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
integrin alpha-6 precursor (vla-6) (cd49f). [source:swissprot;acc:p23229]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3159\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TNRC6A\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
trinucleotide repeat containing 6; edie; gw182 autoantigen. [source:refseq;acc:nm\_014494]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3160\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CCNK\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
cyclin k. [source:swissprot;acc:o75909]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3161\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
BRAP\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
brca1 associated protein. [source:refseq;acc:nm\_006768]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3162\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PEBP1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
phosphatidylethanolamine-binding protein (pebp) (prostatic binding protein) (hcnppp) (neuropolypeptide h3) (raf kinase inhibitor protein) (rkip) [contains: hippocampal cholinergic neurostimulating peptide (hcnp)]. [source:swissprot;acc:p30086]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3163\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CNOT3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [source:refseq;acc:nm\_014516]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3164\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TFAP2C\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [source:swissprot;acc:q92754]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3165\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PIGS\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [source:swissprot;acc:q96s52]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3166\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
MTMR2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
myotubularin-related protein 2 (ec 3.1.3.-). [source:swissprot;acc:q13614]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3167\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ZW10\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
centromere/kinetochore protein zw10 homolog. [source:swissprot;acc:o43264]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3168\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TMED2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
cop-coated vesicle membrane protein p24 precursor (p24a). [source:swissprot;acc:q15363]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3169\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
NFX1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [source:swissprot;acc:q12986]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3170\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
EVI1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ecotropic virus integration 1 site protein. [source:swissprot;acc:q03112]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3171\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CCNT2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
cyclin t2. [source:swissprot;acc:o60583]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3172\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
LIPE\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
hormone sensitive lipase (ec 3.1.1.-) (hsl). [source:swissprot;acc:q05469]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3173\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PIK3C3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [source:refseq;acc:nm\_002647]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3174\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TM9SF3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [source:swissprot;acc:q9hd45]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3175\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TUBA3D\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
tubulin alpha-3/alpha-7 chain (alpha-tubulin 3/7). [source:swissprot;acc:p05214]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3176\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SLC25A3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
phosphate carrier protein, mitochondrial precursor (ptp). [source:swissprot;acc:q00325]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3177\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
LMAN1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [source:swissprot;acc:p49257]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3178\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
transcription initiation factor iie, beta subunit (tfiie-beta). [source:swissprot;acc:p29084]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3179\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
DERL2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
carcinoma related gene. [source:refseq;acc:nm\_016041]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3180\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
HSD17B10\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [source:swissprot;acc:q99714]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3181\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ALDH3A2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [source:swissprot;acc:p51648]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3182\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TCF3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [source:swissprot;acc:p15923]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3183\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CBFB\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [source:swissprot;acc:q13951]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3184\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SP100\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [source:swissprot;acc:p23497]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3185\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
FECH\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [source:swissprot;acc:p22830]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3186\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PRKCQ\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [source:swissprot;acc:q04759]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3187\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
DMRT3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [source:refseq;acc:nm\_021240]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3188\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
WISP2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
connective tissue growth factor-like protein precursor (ctgf-l) (wnt1 inducible signaling pathway protein 2) (wisp-2) (connective tissue growth factor-related protein 58). [source:swissprot;acc:o76076]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3189\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
RNF4\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ring finger protein 4. [source:swissprot;acc:p78317]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3190\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
MTMR1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
myotubularin-related protein 1 (ec 3.1.3.-). [source:swissprot;acc:q13613]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3191\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
APPBP2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [source:refseq;acc:nm\_006380]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3192\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
USP13\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [source:swissprot;acc:q92995]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3193\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
GDI2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [source:swissprot;acc:p50395]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3194\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
MSH4\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
muts protein homolog 4. [source:swissprot;acc:o15457]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3195\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ITGB3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [source:swissprot;acc:p05106]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3196\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
HERPUD1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [source:swissprot;acc:q15011]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3197\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CLPTM1L\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
cisplatin resistance related protein crr9p. [source:refseq;acc:nm\_030782]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3198\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
DCUN1D1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
rp42 homolog; squamous cell carcinoma-related oncogene. [source:refseq;acc:nm\_020640]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3199\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
C6\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
complement component c6 precursor. [source:swissprot;acc:p13671]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3200\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ZFYVE16\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
endosome-associated fyve-domain protein. [source:refseq;acc:nm\_014733]\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/