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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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 2913 to 2962 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
2913\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [source:refseq;acc:nm\_001698]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2914\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
lactamase, beta 2. [source:refseq;acc:nm\_016027]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2915\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitochondrial solute carrier protein. [source:refseq;acc:nm\_016612]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2916\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [source:swissprot;acc:p09329]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2917\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [source:swissprot;acc:p40227]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2918\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nipsnap2 protein (glioblastoma amplified sequence). [source:swissprot;acc:o75323]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2919\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [source:swissprot;acc:p23415]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2920\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
glycine receptor alpha-3 chain precursor. [source:swissprot;acc:o75311]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2921\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [source:refseq;acc:nm\_018456]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2922\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [source:swissprot;acc:o75891]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2923\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transmembrane protein 4. [source:refseq;acc:nm\_014255]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2924\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [source:refseq;acc:nm\_005444]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2925\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ras-related protein ral-b. [source:swissprot;acc:p11234]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2926\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [source:swissprot;acc:o75319]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2927\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
wd-repeat containing protein ciao 1. [source:swissprot;acc:o76071]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2928\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
calmodulin. [source:swissprot;acc:p02593]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2929\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
lysosomal trafficking regulator (beige homolog). [source:swissprot;acc:q99698]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2930\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [source:refseq;acc:nm\_004515]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2931\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [source:swissprot;acc:p06753]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2932\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
pogo transposable element with znf domain isoform 1. [source:refseq;acc:nm\_015100]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2933\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
semaphorin 6c precursor (semaphorin y) (sema y). [source:swissprot;acc:q9h3t2]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2934\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protoporphyrinogen oxidase (ec 1.3.3.4) (ppo). [source:swissprot;acc:p50336]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2935\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
putative membrane protein. [source:refseq;acc:nm\_019026]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2936\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
retinoic acid receptor rxr-gamma. [source:swissprot;acc:p48443]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2937\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
similar to mob-lak. [source:refseq;acc:nm\_145279]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2938\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [source:swissprot;acc:o00622]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2939\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
fibrillin 3. [source:refseq;acc:nm\_032447]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2940\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [source:swissprot;acc:p15884]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2941\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [source:swissprot;acc:q92750]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2942\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [source:swissprot;acc:q15532]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2943\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
phosphoribosyl pyrophosphate synthetase-associated protein 2 (prpp synthetase-associated protein 2) (41 kda phosphoribosypyrophosphate synthetase-associated protein) (pap41). [source:swissprot;acc:o60256]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2944\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tigger transposable element derived 7; jerky (mouse) homolog-like. [source:refseq;acc:nm\_033208]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2945\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tropomyosin 1 alpha chain (alpha-tropomyosin). [source:swissprot;acc:p09493]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2946\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription initiation factor iia gamma chain (tfiia p12 subunit) (tfiia-12) (tfiias) (tfiia-gamma). [source:swissprot;acc:p52657]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2947\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
small edrk-rich factor 2. [source:refseq;acc:nm\_005770]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2948\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [source:swissprot;acc:q99081]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2949\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
microfibrillar-associated protein 1. [source:swissprot;acc:p55081]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2950\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [source:swissprot;acc:p55061]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2951\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
integrin beta-7 precursor. [source:swissprot;acc:p26010]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2952\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
serine/threonine-protein kinase receptor r3 precursor (ec 2.7.1.37) (skr3) (activin receptor-like kinase 1) (alk-1) (tgf-b superfamily receptor type i) (tsr-i). [source:swissprot;acc:p37023]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2953\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
glioma pathogenesis-related protein (glipr) (rtvp-1 protein). [source:swissprot;acc:p48060]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2954\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [source:swissprot;acc:q16795]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2955\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
fibrillin 2 precursor. [source:swissprot;acc:p35556]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2956\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein transport protein sec24b (sec24-related protein b). [source:swissprot;acc:o95487]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2957\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [source:swissprot;acc:q07075]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2958\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ccr4-not transcription complex, subunit 6-like. [source:refseq;acc:nm\_144571]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2959\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
60s ribosomal protein l37a. [source:swissprot;acc:p12751]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2960\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
aldehyde oxidase (ec 1.2.3.1). [source:swissprot;acc:q06278]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2961\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ras-related protein rab-1a (ypt1-related protein). [source:swissprot;acc:p11476]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2962\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dynein 2 light intermediate chain. [source:refseq;acc:nm\_016008]\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/