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

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/