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.


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Gene Network Comparison Type Rank description Value Type Interaction Map Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 25824 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
green
network_comparison
red
251 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Squared 52992.1 1.30521 69165.6
max protein. [swissprot;acc:p25912] Rooted 63.7148 1.13159 56.3054
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Ranked 166.661 1.11707 186.172
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Measured 7859.6 1.22477 6417.18
252 crk-like protein. [swissprot;acc:p46109]
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked 212.457 1.11689 237.292
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 58.4422 1.13099 51.6736
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Squared 52991.7 1.3052 69165
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 204.333 1.11583 228
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured 7859.59 1.22477 6417.18
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 60.465 1.12817 53.5956
254 proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Measured 7859.6 1.22477 6417.18
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 60.4452 1.12756 53.607
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Ranked 179.88 1.11569 200.691
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Squared 52991.7 1.3052 69165
255 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 52967 1.30503 69123.3
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked 179.88 1.11569 200.691
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Measured 7859.6 1.22477 6417.18
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Rooted 70.8854 1.12694 62.9007
256 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 54.0843 1.12665 48.0045
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Squared 20151 1.303 15465.1
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 7859.51 1.22476 6417.19
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Ranked 204.357 1.11569 227.999
257 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Rooted 45.8409 1.12591 51.6125
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Measured 7858.12 1.22452 6417.31
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 179.88 1.11569 200.691
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared 20162.4 1.30229 15482.3
258 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Measured 7857.93 1.22449 6417.33
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Squared 58889.7 1.29799 76438
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Ranked 204.366 1.11564 227.999
thrombospondin 3 precursor. [swissprot;acc:p49746] Rooted 45.8422 1.12589 51.6132
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 58841.7 1.29773 76360.8
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Ranked 204.37 1.11562 227.999
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Measured 7852.52 1.22355 6417.81
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted 65.5926 1.12516 58.2964
260 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Ranked 196.978 1.11394 219.421
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Squared 58801.6 1.29752 76296.4
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Rooted 66.4332 1.12417 59.0951
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured 5193.42 1.22343 4244.95
261 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Ranked 196.978 1.11394 219.421
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Squared 62245.6 1.29334 48127.9
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Rooted 70.0738 1.12417 62.3337
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured 5192.61 1.22255 4247.36
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] 20431.7 1.21852 24896.4
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Ranked 196.978 1.11394 219.421
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Squared 20236.2 1.29261 26157.6
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted 66.7002 1.12276 59.4073
263 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Squared 20236.2 1.29261 26157.6
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Ranked 196.978 1.11394 219.421

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/