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.


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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 [...,...].
Rank Gene Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 1764 to 1813 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
network_comparison
red
green
882 Subtracted TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 8.121 198.781 190.66
883 Divided GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 1.03917 227.596 219.017
Subtracted PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 8.121 198.781 190.66
884 Divided 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] 1.03917 227.596 219.017
Subtracted 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] 8.101 232.473 224.372
885 Divided 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] 1.03917 227.596 219.017
Subtracted no value casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] 8.101 232.473 224.372
886 Divided ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 1.03917 227.596 219.018
Subtracted no value transcription factor btf3 homolog 3. [swissprot;acc:q13892] 8.076 211.908 203.832
887 Divided TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] 1.03913 244.155 234.96
Subtracted PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 8.048 212.002 203.954
888 Divided no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 1.03909 212.027 204.05
Subtracted PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 8.048 212.002 203.954
889 Divided no value alpha-nac protein. [sptrembl;acc:q9h009] 1.03908 212.028 204.053
Subtracted PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 8.048 212.002 203.954
890 Divided STX7 syntaxin 7. [swissprot;acc:o15400] 1.03908 217.181 209.012
Subtracted PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 8.048 212.002 203.954
891 Divided DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] 1.03907 212.028 204.055
Subtracted PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 8.048 212.002 203.954
892 Divided DIRAS2 di-ras2. [refseq;acc:nm_017594] 1.03907 212.028 204.055
Subtracted PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 8.048 212.002 203.954
893 Divided MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 1.03903 227.585 219.037
Subtracted PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 8.048 212.002 203.954
894 Divided FARSA phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 1.03902 217.491 209.323
Subtracted MRPL27 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] 8.042 231.163 239.205
895 Divided FARS2 phenylalanine-trna synthetase. [refseq;acc:nm_006567] 1.03902 217.491 209.323
Subtracted ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 8.039 164 155.961
896 Divided POLR2J dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 1.03888 230.811 239.785
Subtracted WDR36 t-cell activation wd repeat protein. [refseq;acc:nm_139281] 8.018 243.34 235.322
897 Divided PDPK1 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 1.03882 272.878 283.472
Subtracted TGS1 prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] 8.015 210.863 218.878
898 Divided no value 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 1.03874 229.171 238.048
Subtracted 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] 8.015 210.863 218.878
899 Divided TXNDC2 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] 1.03874 229.171 238.048
Subtracted no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 7.977 212.027 204.05
900 Divided TXN thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] 1.03874 229.171 238.048
Subtracted no value alpha-nac protein. [sptrembl;acc:q9h009] 7.975 212.028 204.053
901 Divided 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] 1.03872 237.62 228.762
Subtracted DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] 7.973 212.028 204.055
902 Divided SUPT16H chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] 1.03872 237.62 228.762
Subtracted DIRAS2 di-ras2. [refseq;acc:nm_017594] 7.973 212.028 204.055
903 Divided EIF3G eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 1.03849 246.354 237.223
Subtracted no value uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 7.961 217.168 209.207
904 Divided EIF3A eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] 1.03849 246.354 237.223
Subtracted CIRH1A cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 7.961 243.312 235.351
905 Divided 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] 1.03841 230.768 239.632
Subtracted ero1-like. [refseq;acc:nm_014584] 7.961 217.168 209.207
906 Divided 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] 1.03838 230.764 239.62
Subtracted RSL1D1 pbk1 protein. [sptrembl;acc:o76021] 7.959 243.312 235.353
907 Divided JUP junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] 1.03827 223.906 215.653

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/