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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1762 to 1811 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
881 MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Divided 227.604 219.001 1.03928
882 MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] 227.601 219.008 1.03924
TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Subtracted 198.781 190.66 8.121
883 GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Divided 227.596 219.017 1.03917
PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Subtracted 198.781 190.66 8.121
884 no value ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Divided 227.596 219.017 1.03917
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 232.473 224.372 8.101
885 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
NDUFS8 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 227.596 219.017 1.03917
886 no value transcription factor btf3 homolog 3. [swissprot;acc:q13892] Subtracted 211.908 203.832 8.076
ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Divided 227.596 219.018 1.03917
887 PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Subtracted 212.002 203.954 8.048
TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Divided 244.155 234.96 1.03913
888 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 212.027 204.05 1.03909
PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Subtracted 212.002 203.954 8.048
889 no value alpha-nac protein. [sptrembl;acc:q9h009] Divided 212.028 204.053 1.03908
PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Subtracted 212.002 203.954 8.048
890 PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]
STX7 syntaxin 7. [swissprot;acc:o15400] Divided 217.181 209.012 1.03908
891 DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] 212.028 204.055 1.03907
PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Subtracted 212.002 203.954 8.048
892 DIRAS2 di-ras2. [refseq;acc:nm_017594] Divided 212.028 204.055 1.03907
PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Subtracted 212.002 203.954 8.048
893 MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Divided 227.585 219.037 1.03903
PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Subtracted 212.002 203.954 8.048
894 FARSA phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Divided 217.491 209.323 1.03902
MRPL27 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Subtracted 231.163 239.205 8.042
895 ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 164 155.961 8.039
FARS2 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Divided 217.491 209.323 1.03902
896 POLR2J dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 230.811 239.785 1.03888
WDR36 t-cell activation wd repeat protein. [refseq;acc:nm_139281] Subtracted 243.34 235.322 8.018
897 PDPK1 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Divided 272.878 283.472 1.03882
TGS1 prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Subtracted 210.863 218.878 8.015
898 no value 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Divided 229.171 238.048 1.03874
GOPC 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 210.863 218.878 8.015
899 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 212.027 204.05 7.977
TXNDC2 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Divided 229.171 238.048 1.03874
900 no value alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 212.028 204.053 7.975
TXN thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Divided 229.171 238.048 1.03874
901 DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Subtracted 212.028 204.055 7.973
SSRP1 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 237.62 228.762 1.03872
902 DIRAS2 di-ras2. [refseq;acc:nm_017594] Subtracted 212.028 204.055 7.973
SUPT16H chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Divided 237.62 228.762 1.03872
903 no value uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Subtracted 217.168 209.207 7.961
EIF3G eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Divided 246.354 237.223 1.03849
904 CIRH1A cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Subtracted 243.312 235.351 7.961
EIF3A eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Divided 246.354 237.223 1.03849
905 no value 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] 230.768 239.632 1.03841
ero1-like. [refseq;acc:nm_014584] Subtracted 217.168 209.207 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 230.764 239.62 1.03838

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
- Hugo is the HGNC identifier if it exists
- 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/