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.


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 2001 to 2050 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
251 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Rooted 0 21.3142 23.5833 1.10646
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Squared 1 69165.6 52992.1 1.30521
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Ranked 0 10551.6 11573.6 1.09686
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Measured 1225.08 1079.38 1.13498
max protein. [swissprot;acc:p25912] Rooted 1 56.3054 63.7148 1.13159
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Ranked 186.172 166.661 1.11707
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Measured 6417.18 7859.6 1.22477
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Squared 0 25574.2 20063.8 1.27464
252 crk-like protein. [swissprot;acc:p46109] Measured 1 6417.18 7859.6 1.22477
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked 237.292 212.457 1.11689
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 0 10551.6 11573.5 1.09685
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Rooted 21.1331 19.1063 1.10608
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 1 51.6736 58.4422 1.13099
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Squared 69165 52991.7 1.3052
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] 0 803.941 631.169 1.27373
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Measured 1225.08 1079.38 1.13498
253 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Squared 1 69165 52991.7 1.3052
espin. [refseq;acc:nm_031475] Measured 0 1225.07 1079.38 1.13498
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Ranked 10551.6 11573.5 1.09685
mad protein (max dimerizer). [swissprot;acc:q05195] 1 228 204.333 1.11583
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Squared 0 46977 36903.3 1.27298
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured 1 6417.18 7859.59 1.22477
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Rooted 0 8.05424 8.90701 1.10588
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1 53.5956 60.465 1.12817
254 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Measured 0 1318.22 1495.66 1.13461
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Squared 220.878 173.801 1.27087
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Ranked 10551.6 11573.5 1.09685
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Measured 1 6417.18 7859.6 1.22477
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Rooted 0 8.05424 8.90701 1.10588
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1 53.607 60.4452 1.12756
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Ranked 200.691 179.88 1.11569
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Squared 69165 52991.7 1.3052
255 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Measured 0 1317.84 1495.22 1.1346
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Squared 1 69123.3 52967 1.30503
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Rooted 0 28.4183 31.4149 1.10545
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Squared 220.837 280.438 1.26989
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked 1 200.691 179.88 1.11569
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Measured 6417.18 7859.6 1.22477
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Rooted 62.9007 70.8854 1.12694
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Ranked 0 10551.6 11573.5 1.09685
256 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Rooted 1 48.0045 54.0843 1.12665
espin. [refseq;acc:nm_031475] Ranked 0 10551.6 11573.4 1.09684
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Squared 1 15465.1 20151 1.303
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 0 4766.78 3763.9 1.26645
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Rooted 24.8155 27.4116 1.10462
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Measured 1 6417.19 7859.51 1.22476
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 0 1224.65 1079.77 1.13418
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Ranked 1 227.999 204.357 1.11569
257 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Rooted 0 21.1374 23.3445 1.10442
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 1 51.6125 45.8409 1.12591

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/