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 [...,...].
Network Comparison Type Rank Gene Hugo description Interaction Map Value Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 262 to 311 of 473 in total 
Network Comparison Type: Subtracted
Interaction Map: High confidence
Value Type: Ranked
Filtered: 1
red: 0
green: 0
network\_comparison: 0

\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
3017\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
LRRFIP1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
leucine rich repeat (in flii) interacting protein 1. [source:refseq;acc:nm\_004735]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3018\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CRISP1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [source:swissprot;acc:p54107]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3019\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
KLHDC3\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
testis intracellular mediator protein. [source:refseq;acc:nm\_057161]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3020\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PACSIN1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
protein kinase c and casein kinase substrate in neurons protein 1. [source:swissprot;acc:q9by11]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3021\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CRISP2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [source:swissprot;acc:p16562]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3022\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
NAGK\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [source:swissprot;acc:q9uj70]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3023\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
VAPB\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [source:swissprot;acc:o95292]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3024\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PIGT\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
phosphatidylinositol glycan class t precursor. [source:refseq;acc:nm\_015937]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3025\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
HMG1L1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [source:sptrembl;acc:q9nqj4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3026\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SLC36A1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [source:refseq;acc:nm\_078483]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3027\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
TSFM\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [source:swissprot;acc:p43897]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3028\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
C13orf1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
clll6 protein. [source:refseq;acc:nm\_020456]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3029\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
DNAI1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
dynein intermediate chain 1, axonemal (axonemal dynein intermediate chain 1). [source:swissprot;acc:q9ui46]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3030\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
C6orf35\vspace{3pt}}&\parbox{\wcC}{\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
SPOP\vspace{3pt}}&\parbox{\wcC}{\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
LYZL1\vspace{3pt}}&\parbox{\wcC}{\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
GPAM\vspace{3pt}}&\parbox{\wcC}{\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
CRIPT\vspace{3pt}}&\parbox{\wcC}{\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
TGFB3\vspace{3pt}}&\parbox{\wcC}{\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
PGF\vspace{3pt}}&\parbox{\wcC}{\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
VPS4B\vspace{3pt}}&\parbox{\wcC}{\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
\vspace{3pt}}&\parbox{\wcC}{\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\vspace{3pt}}&\parbox{\wcC}{\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
CTGF\vspace{3pt}}&\parbox{\wcC}{\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
TTR\vspace{3pt}}&\parbox{\wcC}{\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
NR5A2\vspace{3pt}}&\parbox{\wcC}{\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
TTF2\vspace{3pt}}&\parbox{\wcC}{\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
\vspace{3pt}}&\parbox{\wcC}{\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
MSH6\vspace{3pt}}&\parbox{\wcC}{\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
CD207\vspace{3pt}}&\parbox{\wcC}{\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
ORC2L\vspace{3pt}}&\parbox{\wcC}{\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
STK25\vspace{3pt}}&\parbox{\wcC}{\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
SLC30A3\vspace{3pt}}&\parbox{\wcC}{\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
ACVR1\vspace{3pt}}&\parbox{\wcC}{\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
CYB561D2\vspace{3pt}}&\parbox{\wcC}{\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
PDCD10\vspace{3pt}}&\parbox{\wcC}{\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
HGD\vspace{3pt}}&\parbox{\wcC}{\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
ZNF346\vspace{3pt}}&\parbox{\wcC}{\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
ATP6V0E1\vspace{3pt}}&\parbox{\wcC}{\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
SEC24A\vspace{3pt}}&\parbox{\wcC}{\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
C9\vspace{3pt}}&\parbox{\wcC}{\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
GNPDA1\vspace{3pt}}&\parbox{\wcC}{\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
RNASEN\vspace{3pt}}&\parbox{\wcC}{\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
TTC1\vspace{3pt}}&\parbox{\wcC}{\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
CNOT6\vspace{3pt}}&\parbox{\wcC}{\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\vspace{3pt}}&\parbox{\wcC}{\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
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
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/