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.


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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 875 to 924 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
875 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] PRKAA2 212.002 203.954 1.03946
876 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] PRKAA1
877 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] PRKAB2
878 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] PRKAG3
879 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] PRKAB1
880 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] PRKAG2
881 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] MYCL1 227.604 219.001 1.03928
882 n-myc proto-oncogene protein. [swissprot;acc:p04198] MYCN 227.601 219.008 1.03924
883 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] GABPA 227.596 219.017 1.03917
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
885 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
886 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] ELOVL1 219.018
887 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] TBL3 244.155 234.96 1.03913
888 nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] no value 212.027 204.05 1.03909
889 alpha-nac protein. [sptrembl;acc:q9h009] 212.028 204.053 1.03908
890 syntaxin 7. [swissprot;acc:o15400] STX7 217.181 209.012
891 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] DIRAS1 212.028 204.055 1.03907
892 di-ras2. [refseq;acc:nm_017594] DIRAS2
893 myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] MYC 227.585 219.037 1.03903
894 phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] FARSA 217.491 209.323 1.03902
895 phenylalanine-trna synthetase. [refseq;acc:nm_006567] FARS2
896 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] POLR2J 230.811 239.785 1.03888
897 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] PDPK1 272.878 283.472 1.03882
898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] no value 229.171 238.048 1.03874
899 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] TXNDC2
900 thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] TXN
901 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 237.62 228.762 1.03872
902 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] SUPT16H
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 246.354 237.223 1.03849
904 eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] EIF3A
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] no value 230.768 239.632 1.03841
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] 230.764 239.62 1.03838
907 junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] JUP 223.906 215.653 1.03827
908 tax interaction protein 1. [refseq;acc:nm_014604] no value
909 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] SEPT1 142.077 136.846 1.03823
910 uba/ubx 33.3 kda protein. [swissprot;acc:q04323] no value 217.168 209.207 1.03805
911 ero1-like. [refseq;acc:nm_014584]
912 wd-repeat protein 3. [swissprot;acc:q9unx4] WDR3 243.896 234.96 1.03803
913 prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] TGS1 210.863 218.878 1.03801
914 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
915 trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] TRMU 146.036 140.692 1.03798
916 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] HAO2 232.512 241.288 1.03774
917 parafibromin. [refseq;acc:nm_024529] CDC73 239.704 230.991 1.03772
918 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] SORBS1 212.952 205.292 1.03731
919 midasin (midas-containing protein). [swissprot;acc:q9nu22] MDN1 237.218 228.698 1.03725
920 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] DEAF1 236.741 245.547 1.0372
921 rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] RIOK1
922 map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] MARK1
923 map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] MARK2
924 meiotic recombination protein spo11. [swissprot;acc:q9y5k1] SPO11

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/