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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 3180 to 3228 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
3180\vspace{3pt}}&\parbox{\wcB}{\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}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3181\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [source:swissprot;acc:p51648]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3182\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [source:swissprot;acc:p15923]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3183\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [source:swissprot;acc:q13951]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3184\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [source:swissprot;acc:p23497]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3185\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [source:swissprot;acc:p22830]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3186\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [source:swissprot;acc:q04759]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3187\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [source:refseq;acc:nm\_021240]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3188\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
connective tissue growth factor-like protein precursor (ctgf-l) (wnt1 inducible signaling pathway protein 2) (wisp-2) (connective tissue growth factor-related protein 58). [source:swissprot;acc:o76076]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3189\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ring finger protein 4. [source:swissprot;acc:p78317]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3190\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
myotubularin-related protein 1 (ec 3.1.3.-). [source:swissprot;acc:q13613]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3191\vspace{3pt}}&\parbox{\wcB}{\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}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3192\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [source:swissprot;acc:q92995]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3193\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [source:swissprot;acc:p50395]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3194\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
muts protein homolog 4. [source:swissprot;acc:o15457]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3195\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [source:swissprot;acc:p05106]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3196\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [source:swissprot;acc:q15011]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3197\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cisplatin resistance related protein crr9p. [source:refseq;acc:nm\_030782]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3198\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
rp42 homolog; squamous cell carcinoma-related oncogene. [source:refseq;acc:nm\_020640]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3199\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
complement component c6 precursor. [source:swissprot;acc:p13671]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3200\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
endosome-associated fyve-domain protein. [source:refseq;acc:nm\_014733]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3201\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
recessive polycystic kidney disease protein tg737 homolog. [source:swissprot;acc:q13099]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3202\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ran binding protein 3 isoform ranbp3-d; ran-binding protein-3. [source:refseq;acc:nm\_007322]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3203\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
high mobility group protein 4 (hmg-4) (high mobility group protein 2a) (hmg-2a). [source:swissprot;acc:o15347]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3204\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
vaccinia related kinase 2; vaccinia-related kinase-2. [source:refseq;acc:nm\_006296]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3205\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
rb1-inducible coiled coil protein 1. [source:refseq;acc:nm\_014781]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3206\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [source:swissprot;acc:q9by42]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3207\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
complement component c8 beta chain precursor. [source:swissprot;acc:p07358]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3208\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [source:swissprot;acc:q13761]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3209\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [source:swissprot;acc:p51948]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3210\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
trabid protein. [source:swissprot;acc:q9ugi0]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3211\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [source:swissprot;acc:q07973]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3212\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
rala binding protein 1; rala-binding protein. [source:refseq;acc:nm\_006788]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3213\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [source:swissprot;acc:p40925]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3214\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
bs4 protein (ny-ren-18 antigen). [source:swissprot;acc:q9y5a7]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3215\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
membrane-bound transcription factor site 2 protease (ec 3.4.24.-) (site-2 protease) (sterol-regulatory element-binding proteins intramembrane protease). [source:swissprot;acc:o43462]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3216\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna excision repair protein ercc-1. [source:swissprot;acc:p07992]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3217\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sex comb on midleg homolog 1. [source:refseq;acc:nm\_012236]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3218\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [source:swissprot;acc:q9np71]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3219\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [source:swissprot;acc:q9np79]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3220\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [source:swissprot;acc:q92481]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3221\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [source:swissprot;acc:p43034]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3222\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
aldehyde dehydrogenase 7 (ec 1.2.1.5). [source:swissprot;acc:p43353]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3223\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ras-related protein ral-a. [source:swissprot;acc:p11233]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3224\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [source:swissprot;acc:p26006]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3225\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
heat-shock 20 kda like-protein p20. [source:swissprot;acc:o14558]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3226\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [source:swissprot;acc:q9uiv1]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3227\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [source:swissprot;acc:q05084]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3228\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ezrin-binding partner pace-1 isoform 1. [source:refseq;acc:nm\_020423]\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/