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 2962 to 3011 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
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
\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
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/