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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 986 to 1035 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
247 DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Rooted 47.3621 53.8355 1.13668
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Squared 8875.01 6768.05 1.31131
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Measured 6416.68 7865.15 1.22574
248 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked 237.302 212.41 1.11719
CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Measured 6417.18 7859.6 1.22477
LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Rooted 56.0466 63.4808 1.13264
MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Squared 8875.01 6768.05 1.31131
249 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Measured 6417.18 7859.59 1.22477
BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Rooted 55.5965 62.9349 1.13199
PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Squared 8875.01 6768.05 1.31131
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Ranked 237.302 212.41 1.11719
250 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Measured 6417.18 7859.6 1.22477
CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Squared 69201.8 53013.4 1.30536
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Ranked 237.302 212.41 1.11719
NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Rooted 55.5965 62.9349 1.13199
251 BCL6B 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
HCK 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
MAX max protein. [swissprot;acc:p25912] Rooted 56.3054 63.7148 1.13159
SLC15A1 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
252 CRKL crk-like protein. [swissprot;acc:p46109] Measured 6417.18 7859.6 1.22477
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked 237.292 212.457 1.11689
NFYB 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
PASK pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Squared 69165 52991.7 1.3052
253 ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured 6417.18 7859.59 1.22477
BCL6 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Squared 69165 52991.7 1.3052
MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Ranked 228 204.333 1.11583
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 53.5956 60.465 1.12817
254 FYN 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
SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Squared 69165 52991.7 1.3052
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 53.607 60.4452 1.12756
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Ranked 200.691 179.88 1.11569
255 CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Squared 69123.3 52967 1.30503
FGR 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
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Rooted 62.9007 70.8854 1.12694
STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked 200.691 179.88 1.11569
256 no value 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
CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Rooted 48.0045 54.0843 1.12665
GRAP2 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
MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Ranked 227.999 204.357 1.11569
257 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared 15482.3 20162.4 1.30229
COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Rooted 51.6125 45.8409 1.12591
CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Measured 6417.31 7858.12 1.22452
DDOST 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
258 CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Measured 6417.33 7857.93 1.22449
HIP1 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Squared 76438 58889.7 1.29799
MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Ranked 227.999 204.366 1.11564
THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Rooted 51.6132 45.8422 1.12589
259 COL4A3BP 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
RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Ranked 227.999 204.37 1.11562
TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted 58.2964 65.5926 1.12516

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/