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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Rank Gene Hugo Value Type description 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
Hugo
Value Type
description
red
green
network_comparison
1052 SERPINB8 Squared plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] 20357.7 23353.8 1.14717
1053 no value serpin b11. [swissprot;acc:q96p15]
MPPED2 Measured fetal brain protein 239 (239fb). [swissprot;acc:q15777] 4757.46 5198.91 1.09279
PSMA5 Ranked proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] 207.04 200.84 1.03087
RANBP5 Rooted importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] 62.9727 66.1956 1.05118
1054 no value Ranked 60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 217.263 1.03082
DLX3 Measured homeobox protein dlx-3. [swissprot;acc:o60479] 4757.46 5198.91 1.09279
RANBP6 Rooted ran-gtp binding protein (fragment). [sptrembl;acc:o60518] 62.9646 66.1812 1.05109
SERPINB6 Squared placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] 20357.7 23353.8 1.14717
1055 no value cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
ASNSD1 Ranked hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 219.01 212.468 1.03079
CSE1L Rooted importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 74.1383 77.9257 1.05109
TNK2 Measured activated p21cdc42hs kinase. [refseq;acc:nm_005781] 4757.46 5198.91 1.09279
1056 ATP6V1A Ranked 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] 219.01 212.468 1.03079
KIFC3 Rooted kinesin family member c3. [refseq;acc:nm_005550] 63.3481 66.5681 1.05083
MAP3K7IP2 Measured mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] 4757.46 5198.91 1.09279
SERPINB1 Squared leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] 20357.7 23353.8 1.14717
1057 no value histone deacetylase 2 (hd2). [swissprot;acc:q92769] 28801.7 33039.9 1.14715
ASNS Ranked asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] 219.01 212.468 1.03079
DAZAP1 Rooted daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 61.5291 64.6568 1.05083
TMF1 Measured tata element modulatory factor (tmf). [swissprot;acc:p82094] 5412.23 5913.4 1.0926
1058 ATXN2L Ranked ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 228.105 221.293 1.03078
MCFD2 Squared multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 28801.2 33038.7 1.14713
SCYL1 Measured 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] 5412.23 5913.4 1.0926
ZMIZ1 Rooted retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] 61.529 64.6562 1.05082
1059 no value Ranked ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 228.105 221.293 1.03078
Squared dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 28801.2 33038.6 1.14713
Rooted uridine kinase-like 1. [swissprot;acc:q9nwz5] 61.1919 64.2955 1.05072
TBCC Measured tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] 5719.01 6248.6 1.0926
1060 ACOT9 putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
HDAC1 Squared histone deacetylase 1 (hd1). [swissprot;acc:q13547] 28800.8 33037.5 1.1471
NLK Ranked nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] 218.162 211.648 1.03078
NME3 Rooted nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 74.62 78.3934 1.05057
1061 ERC1 Ranked elks protein. [refseq;acc:nm_015064] 218.162 211.648 1.03078
HNRNPL Squared heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] 59335 68062.6 1.14709
NME2P1 Rooted putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 73.8603 77.5904 1.0505
NUP98 Measured nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] 5412.23 5913.4 1.0926
1062 AMMECR1 ammecr1 protein. [refseq;acc:nm_015365]
NME2 Rooted 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] 73.8553 77.585 1.0505
RPP30 Squared ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] 17511.1 20085.3 1.147
ZNF174 Ranked zinc finger protein 174 (aw-1). [swissprot;acc:q15697] 269.963 278.239 1.03066
1063 no value zinc finger imprinted 2. [swissprot;acc:q9nzv7] 269.96 278.232 1.03064
Rooted 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] 73.8426 77.5711 1.05049
PRKRAP1 Squared protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 2709.8 3107.78 1.14687
RAE1 Measured mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] 5412.23 5913.4 1.0926
1064 no value Squared transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] 31583.4 36221.8 1.14686
DDX43 Measured dead-box protein. [refseq;acc:nm_018665] 5719.01 6248.6 1.0926
TLE2 Rooted transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] 63.2949 66.4799 1.05032
ZNF24 Ranked zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 269.955 278.221 1.03062
1065 no value Squared pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 17134.4 19648.7 1.14674

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
- Hugo is the HGNC identifier if it exists
- 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/