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.

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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 [...,...].

Gene Network Comparison Type green red Value Type Filtered network_comparison Interaction Map description Rank

Results: HTML CSV LaTeX

Showing element 1 to 50 of 3228 in total

Network Comparison Type: Divided
green: 0.00001
red: 0.00001
Value Type: Ranked
Filtered: 1
network\_comparison: 1
Interaction Map: High confidence

\def\wcA{0.33333333333333\textwidth}
\def\wcB{0.33333333333333\textwidth}
\begin{longtable}{|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
description\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
Rank\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [source:swissprot;acc:q15147]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3126\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [source:swissprot;acc:o75891]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2922\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [source:swissprot;acc:p42655]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3088\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [source:swissprot;acc:p15428]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2855\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3079\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [source:refseq;acc:nm\_025193]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3147\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2756\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [source:swissprot;acc:p14060]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2802\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [source:swissprot;acc:q99714]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3180\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2904\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
60s ribosomal protein l37a. [source:swissprot;acc:p12751]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2959\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [source:swissprot;acc:q05084]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3227\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [source:swissprot;acc:p24588]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2788\vspace{3pt}}\\\hline
\parbox{\wcA}{\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}}&\parbox{\wcB}{\vspace{3pt}\noindent
3050\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
adaptor protein with pleckstrin homology and src homology 2 domains. [source:refseq;acc:nm\_020979]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2870\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
aldehyde dehydrogenase 7 (ec 1.2.1.5). [source:swissprot;acc:p43353]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3222\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2992\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
aldehyde oxidase (ec 1.2.3.1). [source:swissprot;acc:q06278]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2960\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
alpha crystallin a chain. [source:swissprot;acc:p02489]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2875\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [source:swissprot;acc:p02511]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3082\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [source:refseq;acc:nm\_024083]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2829\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [source:refseq;acc:nm\_006380]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3191\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [source:swissprot;acc:o95376]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2798\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [source:swissprot;acc:p18859]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2893\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [source:swissprot;acc:o75964]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2834\vspace{3pt}}\\\hline
\parbox{\wcA}{\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}}&\parbox{\wcB}{\vspace{3pt}\noindent
2913\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
ba203i16.1 (hypothetical protein kiaa0970). [source:sptrembl;acc:q9h1w1]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3117\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [source:sptrembl;acc:q9bx39]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2968\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
barrier-to-autointegration factor (breakpoint cluster region protein 1). [source:swissprot;acc:o75531]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2804\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [source:swissprot;acc:p55061]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2950\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bcl-6 interacting corepressor isoform 1. [source:refseq;acc:nm\_017745]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2776\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [source:swissprot;acc:q9ubr1]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3145\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bone morphogenetic protein 5 precursor (bmp-5). [source:swissprot;acc:p22003]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3069\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bone morphogenetic protein 6 precursor (bmp-6). [source:swissprot;acc:p22004]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2896\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [source:swissprot;acc:p18075]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3128\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [source:swissprot;acc:p34820]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2773\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
brca1 associated protein. [source:refseq;acc:nm\_006768]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3161\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bromodomain and phd finger-containing protein 3 (fragment). [source:swissprot;acc:q9uld4]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3149\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bromodomain-containing protein 1 (br140-like protein). [source:swissprot;acc:o95696]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3139\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bs4 protein (ny-ren-18 antigen). [source:swissprot;acc:q9y5a7]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3214\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
bup protein. [source:refseq;acc:nm\_012071]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2911\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
calmodulin. [source:swissprot;acc:p02593]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2928\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
camp responsive element binding protein-like 2. [source:refseq;acc:nm\_001310]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3078\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [source:swissprot;acc:p10644]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3089\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
carcinoma related gene. [source:refseq;acc:nm\_016041]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3179\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [source:swissprot;acc:p23786]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2885\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [source:swissprot;acc:q9hcp0]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2830\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [source:swissprot;acc:p78368]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2986\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [source:swissprot;acc:q9y6m4]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
2901\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
caveolin-1. [source:swissprot;acc:q03135]\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3099\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/