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.
Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the
value_type as 'ranked' since this provides a very robust analysis method.
intercation map as 'high confidence'
network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.
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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX
Showing element 3001 to 3050 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
3001\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
NEDD8\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ubiquitin-like protein nedd8. [source:swissprot;acc:q15843]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3002\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
CCNT1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
cyclin t1 (cyclin t) (cyct1). [source:swissprot;acc:o60563]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3003\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
LRRC6\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
testis specific leucine rich repeat protein. [source:refseq;acc:nm\_012472]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3004\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SNRPN\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [source:swissprot;acc:p14648]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3005\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
NDUFA5\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [source:swissprot;acc:q16718]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3006\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
DGCR8\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
dgcr8 protein (digeorge syndrome critical region 8). [source:swissprot;acc:q8wyq5]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3007\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
YEATS4\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
glioma-amplified sequence-41; numa binding protein 1. [source:refseq;acc:nm\_006530]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3008\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
NUP214\vspace{3pt}}&\parbox{\wcC}{\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
COX6B1\vspace{3pt}}&\parbox{\wcC}{\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
UROD\vspace{3pt}}&\parbox{\wcC}{\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
MCM8\vspace{3pt}}&\parbox{\wcC}{\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
SNRPB\vspace{3pt}}&\parbox{\wcC}{\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
CENPB\vspace{3pt}}&\parbox{\wcC}{\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
SLC25A19\vspace{3pt}}&\parbox{\wcC}{\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
NUP85\vspace{3pt}}&\parbox{\wcC}{\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
MRPS7\vspace{3pt}}&\parbox{\wcC}{\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
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
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/