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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 980 to 1029 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
245 Rooted MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 146.94 167.046 1.13683
246 Measured HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 4252.66 5213.05 1.22583
Ranked EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 1.11748
Squared PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 8875.01 6768.05 1.31131
Rooted no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 146.94 167.046 1.13683
247 Measured WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 6416.68 7865.15 1.22574
Ranked no value rna-binding protein. [refseq;acc:nm_019027] 237.302 212.41 1.11719
Squared PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 8875.01 6768.05 1.31131
Rooted DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 47.3621 53.8355 1.13668
248 Measured CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 6417.18 7859.6 1.22477
Ranked no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 212.41 1.11719
Squared MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 8875.01 6768.05 1.31131
Rooted LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 56.0466 63.4808 1.13264
249 Measured ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 6417.18 7859.59 1.22477
Ranked SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] 237.302 212.41 1.11719
Squared PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 8875.01 6768.05 1.31131
Rooted 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] 55.5965 62.9349 1.13199
250 Measured no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 6417.18 7859.6 1.22477
Ranked HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 237.302 212.41 1.11719
Squared CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 69201.8 53013.4 1.30536
Rooted NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 55.5965 62.9349 1.13199
251 Measured HCK 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
Ranked SLC15A1 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
Squared BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 69165.6 52992.1 1.30521
Rooted MAX max protein. [swissprot;acc:p25912] 56.3054 63.7148 1.13159
252 Measured CRKL crk-like protein. [swissprot;acc:p46109] 6417.18 7859.6 1.22477
Ranked EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 237.292 212.457 1.11689
Squared PASK pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 69165 52991.7 1.3052
Rooted 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] 51.6736 58.4422 1.13099
253 Measured ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 6417.18 7859.59 1.22477
Ranked MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] 228 204.333 1.11583
Squared BCL6 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] 69165 52991.7 1.3052
Rooted SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 53.5956 60.465 1.12817
254 Measured FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 6417.18 7859.6 1.22477
Ranked STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 200.691 179.88 1.11569
Squared SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 69165 52991.7 1.3052
Rooted SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 53.607 60.4452 1.12756
255 Measured FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 6417.18 7859.6 1.22477
Ranked STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 200.691 179.88 1.11569
Squared CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 69123.3 52967 1.30503
Rooted RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 62.9007 70.8854 1.12694
256 Measured 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] 6417.19 7859.51 1.22476
Ranked MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 227.999 204.357 1.11569
Squared no value 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
Rooted CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 48.0045 54.0843 1.12665
257 Measured CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 6417.31 7858.12 1.22452
Ranked 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] 200.691 179.88 1.11569
Squared no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 15482.3 20162.4 1.30229
Rooted COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 51.6125 45.8409 1.12591
258 Measured CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 6417.33 7857.93 1.22449

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/