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 Hugo Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1758 to 1807 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
red
network_comparison
green
879 phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] FARSA Subtracted 217.491 8.168 209.323
880 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] PRKAG2 Divided 212.002 1.03946 203.954
phenylalanine-trna synthetase. [refseq;acc:nm_006567] FARS2 Subtracted 217.491 8.168 209.323
881 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] MYCL1 Divided 227.604 1.03928 219.001
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] BTF3 Subtracted 211.961 8.147 203.814
882 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] TOMM20 198.781 8.121 190.66
n-myc proto-oncogene protein. [swissprot;acc:p04198] MYCN Divided 227.601 1.03924 219.008
883 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] GABPA 227.596 1.03917 219.017
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] PEX19 Subtracted 198.781 8.121 190.66
884 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] no value Divided 227.596 1.03917 219.017
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 8.101 224.372
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] NDUFS8 Divided 227.596 1.03917 219.017
886 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] ELOVL1 219.018
transcription factor btf3 homolog 3. [swissprot;acc:q13892] no value Subtracted 211.908 8.076 203.832
887 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] PRKAG1 212.002 8.048 203.954
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] TBL3 Divided 244.155 1.03913 234.96
888 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] PRKAA2 Subtracted 212.002 8.048 203.954
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] no value Divided 212.027 1.03909 204.05
889 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] PRKAA1 Subtracted 212.002 8.048 203.954
alpha-nac protein. [sptrembl;acc:q9h009] no value Divided 212.028 1.03908 204.053
890 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] PRKAB2 Subtracted 212.002 8.048 203.954
syntaxin 7. [swissprot;acc:o15400] STX7 Divided 217.181 1.03908 209.012
891 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] PRKAG3 Subtracted 212.002 8.048 203.954
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] DIRAS1 Divided 212.028 1.03907 204.055
892 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] PRKAB1 Subtracted 212.002 8.048 203.954
di-ras2. [refseq;acc:nm_017594] DIRAS2 Divided 212.028 1.03907 204.055
893 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] PRKAG2 Subtracted 212.002 8.048 203.954
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] MYC Divided 227.585 1.03903 219.037
894 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] MRPL27 Subtracted 231.163 8.042 239.205
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] FARSA Divided 217.491 1.03902 209.323
895 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] ACADVL Subtracted 164 8.039 155.961
phenylalanine-trna synthetase. [refseq;acc:nm_006567] FARS2 Divided 217.491 1.03902 209.323
896 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] POLR2J 230.811 1.03888 239.785
t-cell activation wd repeat protein. [refseq;acc:nm_139281] WDR36 Subtracted 243.34 8.018 235.322
897 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] PDPK1 Divided 272.878 1.03882 283.472
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] TGS1 Subtracted 210.863 8.015 218.878
898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] no value Divided 229.171 1.03874 238.048
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] GOPC Subtracted 210.863 8.015 218.878
899 nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] no value 212.027 7.977 204.05
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] TXNDC2 Divided 229.171 1.03874 238.048
900 alpha-nac protein. [sptrembl;acc:q9h009] no value Subtracted 212.028 7.975 204.053
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] TXN Divided 229.171 1.03874 238.048
901 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] DIRAS1 Subtracted 212.028 7.973 204.055
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] SSRP1 Divided 237.62 1.03872 228.762
902 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] SUPT16H
di-ras2. [refseq;acc:nm_017594] DIRAS2 Subtracted 212.028 7.973 204.055
903 eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] EIF3G Divided 246.354 1.03849 237.223
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] no value Subtracted 217.168 7.961 209.207
904 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] CIRH1A 243.312 235.351

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/