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 862 to 911 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
862 RPL31 60s ribosomal protein l31. [swissprot;acc:p12947] 234.025 224.958 1.04031
863 CSNK2A1P casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 240.194 230.957 1.03999
864 CSNK2A2 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
865 BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 211.961 203.814 1.03997
866 SRP68 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] 221.306 212.806 1.03994
867 no value 40s ribosomal protein s3a. [swissprot;acc:p49241] 225.689 234.674 1.03981
868 MVD diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] 233.298 242.571 1.03975
869 EXOC4 exocyst complex component sec8. [swissprot;acc:q96a65] 217.762 209.449 1.03969
870 no value transcription factor btf3 homolog 3. [swissprot;acc:q13892] 211.908 203.832 1.03962
871 CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 110.2 114.552 1.03949
872 HNRPK heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] 224.413 233.272 1.03948
873 PRPF4 u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]
874 PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 212.002 203.954 1.03946
875 PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]
876 PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]
877 PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]
878 PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]
879 PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]
880 PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]
881 MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] 227.604 219.001 1.03928
882 MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] 227.601 219.008 1.03924
883 GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 227.596 219.017 1.03917
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]
885 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]
886 ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 219.018
887 TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] 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
889 alpha-nac protein. [sptrembl;acc:q9h009] 212.028 204.053 1.03908
890 STX7 syntaxin 7. [swissprot;acc:o15400] 217.181 209.012
891 DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] 212.028 204.055 1.03907
892 DIRAS2 di-ras2. [refseq;acc:nm_017594]
893 MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 227.585 219.037 1.03903
894 FARSA phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 217.491 209.323 1.03902
895 FARS2 phenylalanine-trna synthetase. [refseq;acc:nm_006567]
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
897 PDPK1 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 272.878 283.472 1.03882
898 no value 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 229.171 238.048 1.03874
899 TXNDC2 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]
900 TXN thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]
901 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] 237.62 228.762 1.03872
902 SUPT16H chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
903 EIF3G eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 246.354 237.223 1.03849
904 EIF3A eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]
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
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 JUP junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] 223.906 215.653 1.03827
908 no value tax interaction protein 1. [refseq;acc:nm_014604]
909 SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 142.077 136.846 1.03823
910 no value uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 217.168 209.207 1.03805
911 ero1-like. [refseq;acc:nm_014584]

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/