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 2930 to 2979 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
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
\parbox{\wcA}{\vspace{3pt}\noindent
2963\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
geranylgeranyl transferase type ii beta subunit (ec 2.5.1.-) (rab geranylgeranyltransferase beta subunit) (rab geranyl- geranyltransferase beta subunit) (rab gg transferase beta) (rab ggtase beta). [source:swissprot;acc:p53611]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2964\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
semaphorin 6d isoform 3 precursor. [source:refseq;acc:nm\_153617]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2965\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [source:swissprot;acc:q9h2y9]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2966\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protease inhibitor 15 preproprotein; 25 kda trypsin inhibitor. [source:refseq;acc:nm\_015886]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2967\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
taube nuss. [source:refseq;acc:nm\_138572]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2968\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [source:sptrembl;acc:q9bx39]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2969\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [source:swissprot;acc:p05549]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2970\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [source:swissprot;acc:p48745]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2971\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna-repair protein complementing xp-a cells (xeroderma pigmentosum group a complementing protein). [source:swissprot;acc:p23025]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2972\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [source:swissprot;acc:q13285]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2973\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [source:swissprot;acc:p05062]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2974\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [source:swissprot;acc:p50750]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2975\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [source:refseq;acc:nm\_016121]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2976\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mo25 protein (cgi-66). [source:swissprot;acc:q9y376]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2977\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [source:swissprot;acc:q02318]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2978\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
integrin alpha-7 precursor. [source:swissprot;acc:q13683]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2979\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
udp-glucuronosyltransferase 2b28 precursor, microsomal (ec 2.4.1.17). [source:swissprot;acc:q9by64]\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/