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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 green red network_comparison
Results: HTML CSV LaTeX Showing element 1768 to 1817 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
884 sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Subtracted 224.372 232.473 8.101
885 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Divided 219.017 227.596 1.03917
886 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 219.018
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Subtracted 203.832 211.908 8.076
887 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 203.954 212.002 8.048
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Divided 234.96 244.155 1.03913
888 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Subtracted 203.954 212.002 8.048
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Divided 204.05 212.027 1.03909
889 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Subtracted 203.954 212.002 8.048
alpha-nac protein. [sptrembl;acc:q9h009] Divided 204.053 212.028 1.03908
890 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Subtracted 203.954 212.002 8.048
syntaxin 7. [swissprot;acc:o15400] Divided 209.012 217.181 1.03908
891 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Subtracted 203.954 212.002 8.048
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Divided 204.055 212.028 1.03907
892 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Subtracted 203.954 212.002 8.048
di-ras2. [refseq;acc:nm_017594] Divided 204.055 212.028 1.03907
893 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Subtracted 203.954 212.002 8.048
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Divided 219.037 227.585 1.03903
894 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Subtracted 239.205 231.163 8.042
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Divided 209.323 217.491 1.03902
895 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Subtracted 155.961 164 8.039
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Divided 209.323 217.491 1.03902
896 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 239.785 230.811 1.03888
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Subtracted 235.322 243.34 8.018
897 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Divided 283.472 272.878 1.03882
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Subtracted 218.878 210.863 8.015
898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Divided 238.048 229.171 1.03874
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Subtracted 218.878 210.863 8.015
899 nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 204.05 212.027 7.977
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Divided 238.048 229.171 1.03874
900 alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 204.053 212.028 7.975
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Divided 238.048 229.171 1.03874
901 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Subtracted 204.055 212.028 7.973
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Divided 228.762 237.62 1.03872
902 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
di-ras2. [refseq;acc:nm_017594] Subtracted 204.055 212.028 7.973
903 eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Divided 237.223 246.354 1.03849
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Subtracted 209.207 217.168 7.961
904 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 235.351 243.312
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Divided 237.223 246.354 1.03849
905 dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] 239.632 230.768 1.03841
ero1-like. [refseq;acc:nm_014584] Subtracted 209.207 217.168 7.961
906 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Divided 239.62 230.764 1.03838
pbk1 protein. [sptrembl;acc:o76021] Subtracted 235.353 243.312 7.959
907 junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Divided 215.653 223.906 1.03827
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Subtracted 218.017 225.976 7.959
908 sedlin. [swissprot;acc:o14582] 121.261 129.219 7.958
tax interaction protein 1. [refseq;acc:nm_014604] Divided 215.653 223.906 1.03827
909 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 136.846 142.077 1.03823

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/