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 1008 to 1057 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
252 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
WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Measured 6417.81 7852.52 1.22355
260 HIP1R huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Squared 76296.4 58801.6 1.29752
HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Ranked 219.421 196.978 1.11394
SCYE1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Rooted 59.0951 66.4332 1.12417
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured 4244.95 5193.42 1.22343
261 HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Ranked 219.421 196.978 1.11394
PC pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Squared 48127.9 62245.6 1.29334
RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Rooted 62.3337 70.0738 1.12417
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured 4247.36 5192.61 1.22255
262 CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Squared 26157.6 20236.2 1.29261
CPSF4 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] Measured 24896.4 20431.7 1.21852
HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Ranked 219.421 196.978 1.11394
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted 59.4073 66.7002 1.12276
263 ADCY6 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Squared 26157.6 20236.2 1.29261
HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Ranked 219.421 196.978 1.11394
KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Measured 24896.4 20431.7 1.21852
PXN paxillin. [swissprot;acc:p49023] Rooted 59.4073 66.7002 1.12276
264 ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Squared 26157.6 20236.2 1.29261
COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Measured 4987.58 4094.57 1.2181
DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked 219.421 196.978 1.11394
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Rooted 66.1122 74.1438 1.12148
265 LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Squared 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/