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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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 [...,...].
Gene Rank description Value Type Network Comparison Type Interaction Map Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 1918 to 1967 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
green
network_comparison
red
1918 endothelial-derived gene 1. [refseq;acc:nm_025205] 200.18 1.01015 202.211
1919 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 185.349 187.231
1920 histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 185.413 1.01013 187.292
1921 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 219.386 1.01012 221.607
1922 centaurin gamma 2. [swissprot;acc:q9upq3] 218.452 1.0101 220.659
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] 198.91 1.01008 196.925
1927 rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] 198.914 1.01006 196.932
1928 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 198.935 1.01001 196.964
1929 enigma protein; lim domain protein. [refseq;acc:nm_005451] 217.574 219.753
1930 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 198.935 196.964
1931 eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] 217.574 219.753
1932 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 198.936 196.965
1933 ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 217.82 1.00998 215.667
1934 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 222.055 1.00995 224.264
1935 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 216.279 218.43
1936 creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] 196.347 198.3
1937 quaking isoform 6. [sptrembl;acc:q9p0x9] 216.279 218.43
1938 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 196.341 1.00994 198.293
1939 peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] 196.319 1.00988 198.258
1940 creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] 196.252 198.19
1941 prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675] 196.319 198.258
1942 j domain protein c21orf55. [swissprot;acc:q9nx36] 1.00987 198.257
1943 megf11 protein. [refseq;acc:nm_032445] 222.147 224.34
1944 megf10 protein. [refseq;acc:nm_032446] 222.148 224.341
1945 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 222.151 224.343
1946 nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] 212.142 1.00986 214.234
1947 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 127.083 1.00984 125.845
1948 15 kda selenoprotein precursor. [swissprot;acc:o60613] 212.432 214.522
1949 rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] 216.663 218.794
1950 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] 213.747 1.00982 215.847
1951 trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] 203.873 205.876
1952 importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] 213.724 1.00981 211.647
1953 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 127.146 1.0098 125.912
1954 voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] 213.703 1.00979 211.632
1955 yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] 1.00978 211.633
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] 213.702 211.632
1963 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 213.703 211.633
1964 rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423]
1965 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 222.258 224.432
1966 oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] 213.703 211.633
1967 choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 213.702 211.632

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/