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

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/