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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7691 to 7740 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1923 kinesin protein. [refseq;acc:nm_032559] Squared 23918.8 26165.3 1.09392
nitrilase 1. [refseq;acc:nm_005600] Rooted 62.8946 64.6999 1.0287
1924 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Squared 24354.4 26641.6 1.09391
centaurin gamma 1. [swissprot;acc:q99490] Ranked 220.659 218.452 1.0101
transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354] Measured 7260.23 7711.3 1.06213
utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] Rooted 62.8946 64.6999 1.0287
1925 bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] Measured 7260.23 7711.29 1.06213
centaurin gamma 3. [swissprot;acc:q96p47] Ranked 220.659 218.452 1.0101
dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941] Rooted 62.8932 64.6981 1.0287
ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] Squared 27035.7 29574.2 1.09389
1926 40s ribosomal protein s20. [swissprot;acc:p17075] 12452.6 13619.9 1.09374
frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] Measured 7260.23 7711.3 1.06213
lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182] Rooted 62.8946 64.6999 1.0287
rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] Ranked 196.925 198.91 1.01008
1927 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Squared 12933.8 14145.9 1.09372
dystrophin. [swissprot;acc:p11532] Rooted 62.8946 64.6999 1.0287
rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] Ranked 196.932 198.914 1.01006
transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478] Measured 7260.23 7711.3 1.06213
1928 angiomotin. [refseq;acc:nm_133265] Rooted 62.8946 64.6999 1.0287
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Ranked 196.964 198.935 1.01001
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Squared 12661.6 13847.2 1.09364
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Measured 7514.8 7980.22 1.06193
1929 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Squared 12828.8 14029.4 1.09359
angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201] Rooted 62.8946 64.6999 1.0287
enigma protein; lim domain protein. [refseq;acc:nm_005451] Ranked 219.753 217.574 1.01001
pxr2b protein. [refseq;acc:nm_016559] Measured 6996.51 7429.18 1.06184
1930 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Squared 12829.2 14029.9 1.09359
alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424] Rooted 62.8946 64.6999 1.0287
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Ranked 196.964 198.935 1.01001
p28 ing5. [refseq;acc:nm_032329] Measured 5784.06 6141.48 1.06179
1931 60s ribosomal protein l12. [swissprot;acc:p30050] Squared 12442.9 13606.9 1.09355
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Ranked 219.753 217.574 1.01001
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Measured 9946.21 9367.66 1.06176
sorting nexin 5. [swissprot;acc:q9y5x3] Rooted 62.2844 60.5473 1.02869
1932 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Ranked 196.965 198.936 1.01001
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Squared 12442.9 13606.9 1.09355
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Measured 10300 9701.33 1.06171
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Rooted 59.6991 58.0344 1.02868
1933 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Squared 12442.9 13606.8 1.09354
conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Measured 10300 9701.33 1.06171
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Ranked 215.667 217.82 1.00998
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] Rooted 60.5071 62.2414 1.02866
1934 eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] Squared 22746.3 24873.5 1.09352
gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Ranked 224.264 222.055 1.00995
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] Rooted 60.5071 62.2414 1.02866
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Measured 5949.31 6313.1 1.06115
1935 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] Ranked 218.43 216.279 1.00995
erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Squared 22746.3 24873.5 1.09352
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Rooted 60.5071 62.2414 1.02866
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Measured 6167.29 6544.12 1.0611

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
- 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/