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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 3030 to 3079 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{0.33333333333333\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
3030\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
uncharacterized bone marrow protein bm033. [source:refseq;acc:nm\_018452]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3031\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
speckle-type poz protein. [source:swissprot;acc:o43791]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3032\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm\_032517]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3033\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
glycerol-3-phosphate acyltransferase, mitochondrial precursor (ec 2.3.1.15) (gpat). [source:swissprot;acc:q9hcl2]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3034\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
postsynaptic protein cript; hspc139 protein. [source:refseq;acc:nm\_014171]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3035\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transforming growth factor beta 3 precursor (tgf-beta 3). [source:swissprot;acc:p10600]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3036\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
placenta growth factor precursor (plgf). [source:swissprot;acc:p49763]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3037\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
skd1 protein (vacuolar sorting protein 4b). [source:swissprot;acc:o75351]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3038\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [source:swissprot;acc:q13813]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3039\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [source:swissprot;acc:q01105]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3040\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [source:swissprot;acc:p29279]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3041\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [source:swissprot;acc:p02766]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3042\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
orphan nuclear receptor nr5a2 (alpha-1-fetoprotein transcription factor) (hepatocytic transcription factor) (b1-binding factor) (hb1f) (cyp7a promoter binding factor). [source:swissprot;acc:o00482]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3043\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription termination factor, rna polymerase ii; lodestar protein. [source:refseq;acc:nm\_003594]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3044\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [source:swissprot;acc:q9y2q5]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3045\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [source:swissprot;acc:p52701]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3046\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
langerhans cell specific c-type lectin. [source:refseq;acc:nm\_015717]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3047\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
origin recognition complex subunit 2. [source:swissprot;acc:q13416]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3048\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
serine/threonine protein kinase 25 (ec 2.7.1.37) (sterile 20/oxidant stress-response kinase 1) (ste20/oxidant stress response kinase-1) (sok-1) (ste20-like kinase). [source:swissprot;acc:o00506]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3049\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
zinc transporter 3 (znt-3). [source:swissprot;acc:q99726]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3050\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [source:swissprot;acc:q04771]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3051\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
putative tumor suppressor 101f6. [source:refseq;acc:nm\_007022]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3052\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
programmed cell death 10; apoptosis-related protein 15. [source:refseq;acc:nm\_007217]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3053\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3054\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
double-stranded rna-binding zinc finger protein jaz. [source:refseq;acc:nm\_012279]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3055\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase m9.2 subunit) (v-atpase 9.2 kda membrane accessory protein). [source:swissprot;acc:o15342]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3056\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein transport protein sec24a (sec24-related protein a) (fragment). [source:swissprot;acc:o95486]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3057\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
complement component c9 precursor. [source:swissprot;acc:p02748]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3058\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3059\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [source:swissprot;acc:q9nrr4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3060\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tetratricopeptide repeat protein 1 (tpr repeat protein 1). [source:swissprot;acc:q99614]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3061\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
kiaa1194. [source:refseq;acc:nm\_015455]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3062\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [source:swissprot;acc:p09486]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3063\vspace{3pt}}&\parbox{\wcB}{\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
complement component c7 precursor. [source:swissprot;acc:p10643]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3065\vspace{3pt}}&\parbox{\wcB}{\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
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
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
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
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
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
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
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
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
tu12b1-ty protein. [source:refseq;acc:nm\_016575]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3075\vspace{3pt}}&\parbox{\wcB}{\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
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
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
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
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
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/