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.

Navigation/Query Panel:
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 description Value Type Network Comparison Type Interaction Map red Filtered green network_comparison

Results: HTML CSV LaTeX

Showing element 380 to 429 of 473 in total

Value Type: Ranked
Network Comparison Type: Subtracted
Interaction Map: High confidence
red: 0
Filtered: 1
green: 0
network\_comparison: 0

\def\wcA{0.33333333333333\textwidth}
\def\wcB{0.33333333333333\textwidth}
\begin{longtable}{|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
description\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3135\vspace{3pt}}&\parbox{\wcB}{\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
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
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
hcdi protein. [source:refseq;acc:nm\_020195]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3139\vspace{3pt}}&\parbox{\wcB}{\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
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
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
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
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
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
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
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
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
muts protein homolog 5. [source:swissprot;acc:o43196]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3149\vspace{3pt}}&\parbox{\wcB}{\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
cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [source:swissprot;acc:p54108]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3151\vspace{3pt}}&\parbox{\wcB}{\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
histone deacetylase 6 (hd6). [source:swissprot;acc:q9ubn7]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3153\vspace{3pt}}&\parbox{\wcB}{\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
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
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
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
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
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
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
cyclin k. [source:swissprot;acc:o75909]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3161\vspace{3pt}}&\parbox{\wcB}{\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
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
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
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
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
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
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
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
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
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
cyclin t2. [source:swissprot;acc:o60583]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3172\vspace{3pt}}&\parbox{\wcB}{\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
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
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
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
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
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
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
carcinoma related gene. [source:refseq;acc:nm\_016041]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3180\vspace{3pt}}&\parbox{\wcB}{\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
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
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
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
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [source:swissprot;acc:p23497]\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

 - 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/