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.


Navigation/Query Panel:
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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1913 to 1962 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
green
network_comparison
1913 phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 215.745 213.564 1.01021
1914 phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2]
1915 phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] 215.747 213.571 1.01019
1916 rh type c glycoprotein. [refseq;acc:nm_016321] 196.88 198.88 1.01016
1917 p28 ing5. [refseq;acc:nm_032329] 215.848 218.039 1.01015
1918 endothelial-derived gene 1. [refseq;acc:nm_025205] 202.211 200.18
1919 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 187.231 185.349
1920 histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 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
1922 centaurin gamma 2. [swissprot;acc:q9upq3] 220.659 218.452 1.0101
1923 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763]
1924 centaurin gamma 1. [swissprot;acc:q99490]
1925 centaurin gamma 3. [swissprot;acc:q96p47]
1926 rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] 196.925 198.91 1.01008
1927 rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] 196.932 198.914 1.01006
1928 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 196.964 198.935 1.01001
1929 enigma protein; lim domain protein. [refseq;acc:nm_005451] 219.753 217.574
1930 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 196.964 198.935
1931 eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] 219.753 217.574
1932 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 196.965 198.936
1933 ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 215.667 217.82 1.00998
1934 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 224.264 222.055 1.00995
1935 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 218.43 216.279
1936 creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] 198.3 196.347
1937 quaking isoform 6. [sptrembl;acc:q9p0x9] 218.43 216.279
1938 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 198.293 196.341 1.00994
1939 peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] 198.258 196.319 1.00988
1940 creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] 198.19 196.252
1941 prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675] 198.258 196.319
1942 j domain protein c21orf55. [swissprot;acc:q9nx36] 198.257 1.00987
1943 megf11 protein. [refseq;acc:nm_032445] 224.34 222.147
1944 megf10 protein. [refseq;acc:nm_032446] 224.341 222.148
1945 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 224.343 222.151
1946 nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] 214.234 212.142 1.00986
1947 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 125.845 127.083 1.00984
1948 15 kda selenoprotein precursor. [swissprot;acc:o60613] 214.522 212.432
1949 rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] 218.794 216.663
1950 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] 215.847 213.747 1.00982
1951 trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] 205.876 203.873
1952 importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] 211.647 213.724 1.00981
1953 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 125.912 127.146 1.0098
1954 voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] 211.632 213.703 1.00979
1955 yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] 211.633 1.00978
1956 voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722]
1957 similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557]
1958 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]
1959 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340]
1960 golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799]
1961 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870]
1962 methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] 211.632 213.702

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/