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 1001 to 1050 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
251 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Squared 69165.6 52992.1 1.30521
max protein. [swissprot;acc:p25912] Rooted 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
252 crk-like protein. [swissprot;acc:p46109]
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked 237.292 212.457 1.11689
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] Rooted 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
253 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]
mad protein (max dimerizer). [swissprot;acc:q05195] Ranked 228 204.333 1.11583
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured 6417.18 7859.59 1.22477
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 53.5956 60.465 1.12817
254 proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Measured 6417.18 7859.6 1.22477
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 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 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 69123.3 52967 1.30503
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked 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
256 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 48.0045 54.0843 1.12665
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Squared 15465.1 20151 1.303
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 6417.19 7859.51 1.22476
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Ranked 227.999 204.357 1.11569
257 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Rooted 51.6125 45.8409 1.12591
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Measured 6417.31 7858.12 1.22452
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Ranked 200.691 179.88 1.11569
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared 15482.3 20162.4 1.30229
258 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Measured 6417.33 7857.93 1.22449
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Squared 76438 58889.7 1.29799
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Ranked 227.999 204.366 1.11564
thrombospondin 3 precursor. [swissprot;acc:p49746] Rooted 51.6132 45.8422 1.12589
259 goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Squared 76360.8 58841.7 1.29773
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Ranked 227.999 204.37 1.11562
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Measured 6417.81 7852.52 1.22355
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted 58.2964 65.5926 1.12516
260 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Ranked 219.421 196.978 1.11394
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Squared 76296.4 58801.6 1.29752
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Rooted 59.0951 66.4332 1.12417
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured 4244.95 5193.42 1.22343
261 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Ranked 219.421 196.978 1.11394
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Squared 48127.9 62245.6 1.29334
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Rooted 62.3337 70.0738 1.12417
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured 4247.36 5192.61 1.22255
262 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 24896.4 20431.7 1.21852
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Ranked 219.421 196.978 1.11394
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Squared 26157.6 20236.2 1.29261
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted 59.4073 66.7002 1.12276
263 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Squared 26157.6 20236.2 1.29261
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Ranked 219.421 196.978 1.11394

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/