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.


Navigation/Query Panel:
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 3858 to 3907 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1929 pxr2b protein. [refseq;acc:nm_016559] Divided 6996.51 7429.18 1.06184
1930 coactosin-like protein. [swissprot;acc:q14019] Subtracted 5888.32 6245.89 357.57
p28 ing5. [refseq;acc:nm_032329] Divided 5784.06 6141.48 1.06179
1931 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] 9946.21 9367.66 1.06176
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Subtracted 5888.32 6245.89 357.57
1932 hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Divided 10300 9701.33 1.06171
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Subtracted 5888.32 6245.89 357.57
1933 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Divided 10300 9701.33 1.06171
rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] Subtracted 6218.34 6575.81 357.47
1934 hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] 5514.19 5871.64 357.45
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Divided 5949.31 6313.1 1.06115
1935 p28 ing5. [refseq;acc:nm_032329] Subtracted 5784.06 6141.48 357.42
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Divided 6167.29 6544.12 1.0611
1936 translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Subtracted 5424.3 5781.58 357.28
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Divided 5171.45 5486.96 1.06101
1937 40s ribosomal protein s26. [swissprot;acc:p02383] Subtracted 5488.7 5131.89 356.81
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Divided 5171.45 5486.96 1.06101
1938 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Subtracted 5488.7 5131.89 356.81
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Divided 5171.45 5486.96 1.06101
1939 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Subtracted 5488.7 5131.89 356.81
brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] Divided 5669.9 6015.75 1.061
1940 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] 4450.17 4721.37 1.06094
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Subtracted 5488.7 5131.89 356.81
1941 atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 6064.92 6421.65 356.73
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Divided 5521.07 5856.93 1.06083
1942 c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] Subtracted 5941.24 6297.78 356.54
pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] Divided 5805.06 6158.16 1.06083
1943 p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] 7210.87 7649.23 1.06079
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Subtracted 4977.77 5333.78 356.01
1944 general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] Divided 7210.64 7648.94 1.06079
tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Subtracted 5387.64 5743.5 355.86
1945 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] Divided 6230.21 6608.64 1.06074
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Subtracted 5939.85 6294.91 355.06
1946 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281] Divided 6230.21 6608.64 1.06074
pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] Subtracted 5805.06 6158.16 353.1
1947 carboxypeptidase a5. [refseq;acc:nm_080385] 8353.97 8001.45 352.52
transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542] Divided 7195.76 7632.83 1.06074
1948 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Subtracted 8353.97 8001.45 352.52
destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] Divided 6230.21 6608.64 1.06074
1949 neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Subtracted 8353.97 8001.45 352.52
ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] Divided 6230.21 6608.64 1.06074
1950 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Subtracted 8353.97 8001.45 352.52
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Divided 5888.32 6245.89 1.06073
1951 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Subtracted 8353.97 8001.45 352.52
fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Divided 5888.32 6245.89 1.06073
1952 coactosin-like protein. [swissprot;acc:q14019]
paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Subtracted 6318.3 6670.1 351.8
1953 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 4077.89 4428.28 350.39
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Divided 5888.32 6245.89 1.06073
1954 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Subtracted 6101.12 6449.87 348.75

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/