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 Value Type description green Interaction Map red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 25824 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
green
red
network_comparison
251 Measured tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 7859.6 6417.18 1.22477
Ranked oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 166.661 186.172 1.11707
Squared b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 52992.1 69165.6 1.30521
Rooted max protein. [swissprot;acc:p25912] 63.7148 56.3054 1.13159
252 Measured crk-like protein. [swissprot;acc:p46109] 7859.6 6417.18 1.22477
Ranked eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 212.457 237.292 1.11689
Squared pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 52991.7 69165 1.3052
Rooted 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] 58.4422 51.6736 1.13099
253 Measured proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 7859.59 6417.18 1.22477
Ranked mad protein (max dimerizer). [swissprot;acc:q05195] 204.333 228 1.11583
Squared b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] 52991.7 69165 1.3052
Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 60.465 53.5956 1.12817
254 Measured proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 7859.6 6417.18 1.22477
Ranked source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 179.88 200.691 1.11569
Squared zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 52991.7 69165 1.3052
Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 60.4452 53.607 1.12756
255 Measured proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 7859.6 6417.18 1.22477
Ranked oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 179.88 200.691 1.11569
Squared c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 52967 69123.3 1.30503
Rooted ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 70.8854 62.9007 1.12694
256 Measured 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] 7859.51 6417.19 1.22476
Ranked max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 204.357 227.999 1.11569
Squared formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 20151 15465.1 1.303
Rooted ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 54.0843 48.0045 1.12665
257 Measured ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 7858.12 6417.31 1.22452
Ranked 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] 179.88 200.691 1.11569
Squared huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 20162.4 15482.3 1.30229
Rooted cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 45.8409 51.6125 1.12591
258 Measured homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 7857.93 6417.33 1.22449
Ranked max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 204.366 227.999 1.11564
Squared huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 58889.7 76438 1.29799
Rooted thrombospondin 3 precursor. [swissprot;acc:p49746] 45.8422 51.6132 1.12589
259 Measured neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 7852.52 6417.81 1.22355
Ranked max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 204.37 227.999 1.11562
Squared 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] 58841.7 76360.8 1.29773
Rooted tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 65.5926 58.2964 1.12516
260 Measured signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 5193.42 4244.95 1.22343
Ranked c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 196.978 219.421 1.11394
Squared huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 58801.6 76296.4 1.29752
Rooted multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 66.4332 59.0951 1.12417
261 Measured signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 5192.61 4247.36 1.22255
Ranked heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 196.978 219.421 1.11394
Squared pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] 62245.6 48127.9 1.29334
Rooted ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 70.0738 62.3337 1.12417
262 Measured 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 24896.4 1.21852
Ranked heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 196.978 219.421 1.11394
Squared neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 20236.2 26157.6 1.29261
Rooted polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 66.7002 59.4073 1.12276
263 Measured trs85 homolog. [swissprot;acc:q9y2l5] 20431.7 24896.4 1.21852
Ranked heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 196.978 219.421 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/