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 Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 3008 to 3057 of 3228 in total

Value Type: Measured
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
3008\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [source:swissprot;acc:p35658]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3009\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [source:swissprot;acc:p14854]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3010\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [source:swissprot;acc:p06132]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3011\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna replication licensing factor mcm8 (minichromosome maintenance 8). [source:swissprot;acc:q9uja3]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3012\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [source:swissprot;acc:p14678]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3013\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
major centromere autoantigen b (centromere protein b) (cenp-b). [source:swissprot;acc:p07199]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3014\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitochondrial deoxynucleotide carrier (mitochondrial uncoupling protein 1). [source:swissprot;acc:q9hc21]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3015\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
pericentrin 1; frount; nucleoporin nup75. [source:refseq;acc:nm\_024844]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3016\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitochondrial ribosomal protein s7; 30s ribosomal protein s7 homolog. [source:refseq;acc:nm\_015971]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3017\vspace{3pt}}&\parbox{\wcB}{\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
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
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
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
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
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
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
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
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
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
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
clll6 protein. [source:refseq;acc:nm\_020456]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3029\vspace{3pt}}&\parbox{\wcB}{\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
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
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/