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 2980 to 3029 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
2980\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ste20-like kinase; ste2-like kinase. [source:refseq;acc:nm\_016281]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2981\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
zinc finger daz interacting protein 1. [source:refseq;acc:nm\_014934]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2982\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
serine/threonine protein kinase mask; ste20-like kinase mst4. [source:refseq;acc:nm\_016542]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2983\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2984\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
similar to cg5057 gene product. [source:sptrembl;acc:q9btt4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2985\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
myosin heavy chain, smooth muscle isoform (smmhc). [source:swissprot;acc:p35749]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2986\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [source:swissprot;acc:p78368]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2987\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
spartin; trans-activated by hepatitis c virus core protein 1. [source:refseq;acc:nm\_015087]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2988\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
myosin heavy chain, nonmuscle type b (cellular myosin heavy chain, type b) (nonmuscle myosin heavy chain-b) (nmmhc-b). [source:swissprot;acc:p35580]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2989\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
high mobility group protein 1 (hmg-1). [source:swissprot;acc:p09429]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2990\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [source:swissprot;acc:p49336]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2991\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
neuromedin u receptor 2. [source:refseq;acc:nm\_020167]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2992\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2993\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
vacuolar protein sorting factor 4a; skd1-homolog; vacuolar sorting protein 4. [source:refseq;acc:nm\_013245]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2994\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [source:refseq;acc:nm\_016532]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2995\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
t-complex protein 1, zeta-2 subunit (tcp-1-zeta-2) (cct-zeta-2) (tcp- 1-zeta-like) (cct-zeta-like) (testis-specific tcp20) (testis-specific protein tsa303). [source:swissprot;acc:q92526]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2996\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
rna-binding protein 8a (rna binding motif protein 8a) (ribonucleoprotein rbm8a) (rna-binding protein y14) (binder of ovca1- 1) (bov-1). [source:swissprot;acc:q9y5s9]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2997\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
proteasome activator complex subunit 3 (proteasome activator 28-gamma subunit) (pa28gamma) (pa28g) (activator of multicatalytic protease subunit 3) (11s regulator complex gamma subunit) (reg-gamma) (ki nuclear autoantigen). [source:swissprot;acc:q12920]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2998\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
fyve-finger-containing rab5 effector protein rabenosyn-5. [source:refseq;acc:nm\_022340]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2999\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [source:swissprot;acc:o00268]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3000\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
myeloblast kiaa0230 (fragment). [source:sptrembl;acc:q92626]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3001\vspace{3pt}}&\parbox{\wcB}{\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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
clll6 protein. [source:refseq;acc:nm\_020456]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3029\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dynein intermediate chain 1, axonemal (axonemal dynein intermediate chain 1). [source:swissprot;acc:q9ui46]\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/