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 3827 to 3876 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1914 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Subtracted 196.008 198.154 2.146
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] Divided 215.745 213.564 1.01021
1915 phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] 215.747 213.571 1.01019
rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] Subtracted 218.794 216.663 2.131
1916 lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] 225.022 222.9 2.122
rh type c glycoprotein. [refseq;acc:nm_016321] Divided 196.88 198.88 1.01016
1917 p28 ing5. [refseq;acc:nm_032329] 215.848 218.039 1.01015
regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] Subtracted 219.777 217.659 2.118
1918 endothelial-derived gene 1. [refseq;acc:nm_025205] Divided 202.211 200.18 1.01015
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Subtracted 215.847 213.747 2.1
1919 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Divided 187.231 185.349 1.01015
nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] Subtracted 214.234 212.142 2.092
1920 15 kda selenoprotein precursor. [swissprot;acc:o60613] 214.522 212.432 2.09
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Divided 187.292 185.413 1.01013
1921 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 221.607 219.386 1.01012
importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Subtracted 211.647 213.724 2.077
1922 centaurin gamma 2. [swissprot;acc:q9upq3] Divided 220.659 218.452 1.0101
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Subtracted 219.25 217.175 2.075
1923 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Divided 220.659 218.452 1.0101
lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] Subtracted 225.02 222.948 2.072
1924 centaurin gamma 1. [swissprot;acc:q99490] Divided 220.659 218.452 1.0101
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Subtracted 211.632 213.703 2.071
1925 centaurin gamma 3. [swissprot;acc:q96p47] Divided 220.659 218.452 1.0101
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Subtracted 211.633 213.703 2.07
1926 rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] Divided 196.925 198.91 1.01008
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Subtracted 211.633 213.703 2.07
1927 rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] Divided 196.932 198.914 1.01006
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Subtracted 211.633 213.703 2.07
1928 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Divided 196.964 198.935 1.01001
1929 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Subtracted 211.633 213.703 2.07
enigma protein; lim domain protein. [refseq;acc:nm_005451] Divided 219.753 217.574 1.01001
1930 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 196.964 198.935
golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Subtracted 211.633 213.703 2.07
1931 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870]
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Divided 219.753 217.574 1.01001
1932 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 196.965 198.936
methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Subtracted 211.632 213.702 2.07
1933 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 211.633 213.703
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Divided 215.667 217.82 1.00998
1934 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 224.264 222.055 1.00995
rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Subtracted 211.633 213.703 2.07
1935 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] Divided 218.43 216.279 1.00995
oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Subtracted 211.633 213.703 2.07
1936 choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 211.632 213.702
creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] Divided 198.3 196.347 1.00995
1937 quaking isoform 6. [sptrembl;acc:q9p0x9] 218.43 216.279
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Subtracted 211.633 213.703 2.07
1938 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Divided 198.293 196.341 1.00994

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/