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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 4208 to 4257 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1052 small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Rooted 83.0639 87.321 1.05125
1053 fetal brain protein 239 (239fb). [swissprot;acc:q15777] Measured 4757.46 5198.91 1.09279
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Rooted 62.9727 66.1956 1.05118
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Ranked 207.04 200.84 1.03087
serpin b11. [swissprot;acc:q96p15] Squared 20357.7 23353.8 1.14717
1054 60s ribosomal protein l21. [swissprot;acc:p46778] Ranked 223.958 217.263 1.03082
homeobox protein dlx-3. [swissprot;acc:o60479] Measured 4757.46 5198.91 1.09279
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Squared 20357.7 23353.8 1.14717
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Rooted 62.9646 66.1812 1.05109
1055 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Measured 4757.46 5198.91 1.09279
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Squared 20357.7 23353.8 1.14717
hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Ranked 219.01 212.468 1.03079
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Rooted 74.1383 77.9257 1.05109
1056 kinesin family member c3. [refseq;acc:nm_005550] 63.3481 66.5681 1.05083
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Squared 20357.7 23353.8 1.14717
mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Measured 4757.46 5198.91 1.09279
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Ranked 219.01 212.468 1.03079
1057 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Rooted 61.5291 64.6568 1.05083
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Squared 28801.7 33039.9 1.14715
tata element modulatory factor (tmf). [swissprot;acc:p82094] Measured 5412.23 5913.4 1.0926
1058 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Ranked 228.105 221.293 1.03078
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Squared 28801.2 33038.7 1.14713
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Rooted 61.529 64.6562 1.05082
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Measured 5412.23 5913.4 1.0926
1059 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Ranked 228.105 221.293 1.03078
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Squared 28801.2 33038.6 1.14713
tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] Measured 5719.01 6248.6 1.0926
uridine kinase-like 1. [swissprot;acc:q9nwz5] Rooted 61.1919 64.2955 1.05072
1060 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Squared 28800.8 33037.5 1.1471
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Ranked 218.162 211.648 1.03078
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Rooted 74.62 78.3934 1.05057
putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] Measured 5719.01 6248.6 1.0926
1061 elks protein. [refseq;acc:nm_015064] Ranked 218.162 211.648 1.03078
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Squared 59335 68062.6 1.14709
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Measured 5412.23 5913.4 1.0926
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Rooted 73.8603 77.5904 1.0505
1062 ammecr1 protein. [refseq;acc:nm_015365] Measured 5412.23 5913.4 1.0926
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Rooted 73.8553 77.585 1.0505
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Squared 17511.1 20085.3 1.147
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Ranked 269.963 278.239 1.03066
1063 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Measured 5412.23 5913.4 1.0926
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Rooted 73.8426 77.5711 1.05049
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Squared 2709.8 3107.78 1.14687
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Ranked 269.96 278.232 1.03064
1064 dead-box protein. [refseq;acc:nm_018665] Measured 5719.01 6248.6 1.0926
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Rooted 63.2949 66.4799 1.05032
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Squared 31583.4 36221.8 1.14686
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Ranked 269.955 278.221 1.03062
1065 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Measured 6393.81 6984.94 1.09245

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/