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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2036 to 2085 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
255 MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Measured Subtracted 4455.95 5774.03 1318.08
MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Ranked 227.999 204.366 23.633
PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Rooted 132.156 122.835 9.321
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Divided 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
EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 132.114 122.802 9.312
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 Divided 6417.19 7859.51 1.22476
GYS2 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared Subtracted 39463.9 48362.1 8898.2
MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Measured 4456.67 5773.77 1317.1
Ranked Divided 227.999 204.357 1.11569
RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 204.37 23.629
257 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Squared Divided 15482.3 20162.4 1.30229
CMPK ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Ranked Subtracted 242.14 265.697 23.557
COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Rooted Divided 51.6125 45.8409 1.12591
CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 132.467 123.158 9.309
CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Measured Divided 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
MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Measured Subtracted 4456.93 5773.67 1316.74
NME2P1 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Squared 33526 42390.2 8864.2
258 AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Ranked 242.14 265.697 23.557
CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Measured Divided 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
NME2 nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Squared Subtracted 33522.8 42384.8 8862
PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Rooted 132.063 122.761 9.302
RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Measured 4457.06 5773.63 1316.57
THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Rooted Divided 51.6132 45.8422 1.12589
259 no value adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Ranked Subtracted 242.14 265.696 23.556
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Squared 33514.4 42370.8 8856.4
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] Divided 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
SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Rooted Subtracted 107.961 117.197 9.236
SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Measured 4569.48 5885.79 1316.31
TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted Divided 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 CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Subtracted 12515.4 11221.1 1294.3
HIP1R huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Squared Divided 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
MED22 surfeit locus protein 5. [swissprot;acc:q15528] Subtracted 242.14 265.696 23.556
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 Divided 59.0951 66.4332 1.12417
SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Subtracted 56.7592 65.9889 9.2297
SH3GL1 sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Squared 35793 44595.3 8802.3
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured Divided 4244.95 5193.42 1.22343
261 CPA5 carboxypeptidase a5. [refseq;acc:nm_080385] Squared Subtracted 53174 44377.4 8796.6
EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Rooted 52.7582 61.9123 9.1541
HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Ranked Divided 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

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/