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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1000 to 1049 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
250 NOLA1 Rooted nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 55.5965 62.9349 1.13199
251 BCL6B Squared b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 69165.6 52992.1 1.30521
HCK Measured tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 6417.18 7859.6 1.22477
MAX Rooted max protein. [swissprot;acc:p25912] 56.3054 63.7148 1.13159
SLC15A1 Ranked oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 186.172 166.661 1.11707
252 CRKL Measured crk-like protein. [swissprot;acc:p46109] 6417.18 7859.6 1.22477
EIF4G1 Ranked eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 237.292 212.457 1.11689
NFYB 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] 51.6736 58.4422 1.13099
PASK Squared pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 69165 52991.7 1.3052
253 ABL1 Measured proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 6417.18 7859.59 1.22477
BCL6 Squared b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] 69165 52991.7 1.3052
MXD1 Ranked mad protein (max dimerizer). [swissprot;acc:q05195] 228 204.333 1.11583
SRP9 Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 53.5956 60.465 1.12817
254 FYN Measured proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 6417.18 7859.6 1.22477
SNAI2 Squared zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 69165 52991.7 1.3052
SRP9 Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 53.607 60.4452 1.12756
STT3B Ranked source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 200.691 179.88 1.11569
255 CTBP1 Squared c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 69123.3 52967 1.30503
FGR Measured proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 6417.18 7859.6 1.22477
RRM2 Rooted ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 62.9007 70.8854 1.12694
STT3A Ranked oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 200.691 179.88 1.11569
256 no value Squared formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 15465.1 20151 1.303
CEBPZ Rooted ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 48.0045 54.0843 1.12665
GRAP2 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] 6417.19 7859.51 1.22476
MXI1 Ranked max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 227.999 204.357 1.11569
257 no value Squared huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 15482.3 20162.4 1.30229
COMP Rooted cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 51.6125 45.8409 1.12591
CUTL1 Measured ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 6417.31 7858.12 1.22452
DDOST 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] 200.691 179.88 1.11569
258 CUTL2 Measured homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 6417.33 7857.93 1.22449
HIP1 Squared huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 76438 58889.7 1.29799
MXD4 Ranked max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 227.999 204.366 1.11564
THBS3 Rooted thrombospondin 3 precursor. [swissprot;acc:p49746] 51.6132 45.8422 1.12589
259 COL4A3BP 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] 76360.8 58841.7 1.29773
RAB24 Ranked max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 227.999 204.37 1.11562
TFIP11 Rooted tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 58.2964 65.5926 1.12516
WASL Measured neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 6417.81 7852.52 1.22355
260 HIP1R Squared huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 76296.4 58801.6 1.29752
HS3ST6 Ranked c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 219.421 196.978 1.11394
SCYE1 Rooted multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 59.0951 66.4332 1.12417
SRP9 Measured signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 4244.95 5193.42 1.22343
261 HS3ST3A1 Ranked heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 219.421 196.978 1.11394
PC Squared pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] 48127.9 62245.6 1.29334
RRM2B Rooted ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 62.3337 70.0738 1.12417
SRP9 Measured signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 4247.36 5192.61 1.22255
262 CHRNA7 Squared neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 26157.6 20236.2 1.29261
CPSF4 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] 24896.4 20431.7 1.21852
HS3ST3B1 Ranked heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 219.421 196.978 1.11394
POLI Rooted polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 59.4073 66.7002 1.12276
263 ADCY6 Squared adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 26157.6 20236.2 1.29261

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
- Hugo is the HGNC identifier if it exists
- 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/