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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1082 to 1131 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		network_comparison
    		green
    1082 PLEKHF2 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] 220.118 1.03011 213.685
    1083 SRD5A1 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405]
    1084 SRD5A2 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213]
    1085 DKC1 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 231.007 1.02968 237.864
    1086 no value similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 236.679 1.02958 243.679
    1087 zinc finger protein 277. [swissprot;acc:q9nrm2]
    1088 ANXA11 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 219.673 1.0295 213.378
    1089 CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 121.428 1.02945 125.004
    1090 no value similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 226.218 232.88
    1091 block 23. [sptrembl;acc:q8nhw5] 226.205 1.02941 232.858
    1092 RPLP0 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 226.203 232.855
    1093 COPA coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] 177.432 1.02939 182.647
    1094 ANXA7 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] 219.655 1.02938 213.385
    1095 GTPBP3 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] 213.552 1.02935 207.463
    1096 NDUFB9 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 212.345 1.02911 206.339
    1097 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 209.123 203.208
    1098 AP3M1 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] 217.323 1.02906 211.185
    1099 AP3M2 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 217.315 1.02904 211.183
    1100 ATP2C1 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 209.052 1.02889 203.183
    1101 KARS lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] 220.291 1.02857 226.584
    1102 no value 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 229.442 1.02847 235.974
    1103 RPS27L ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 229.441 1.02846 235.972
    1104 HAO1 hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] 231.922 1.0283 238.486
    1105 FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 191.139 1.02828 185.882
    1106 PEX5L pxr2b protein. [refseq;acc:nm_016559] 212.945 1.02818 207.109
    1107 SPTLC2 serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] 204.603 1.02796 210.324
    1108 FOXK2 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006 1.02775 212.119
    1109 TPT1 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] 218.098 212.209
    1110 GIT2 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 216.78 1.02769 222.782
    1111 no value apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 217.99 1.02766 212.123
    1112 HNF4G hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] 251.863 258.829
    1113 GADD45G growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]
    1114 GADD45A growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]
    1115 HNF4A hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235]
    1116 GADD45B growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]
    1117 NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 168.989 1.02754 164.46
    1118 NXF3 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 168.995 1.02753 164.467
    1119 ATP6V0A2 vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] 218.528 1.02752 212.676
    1120 ATP6V0A4 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632]
    1121 ATP6V0A1 vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] 218.529
    1122 TCIRG1 vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] 218.527 1.02751
    1123 NXF1 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 169.031 1.0275 164.507
    1124 PRDX5 peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] 207.553 1.02748 213.256
    1125 no value dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 204.404 210.022
    1126 ATP6V0D2 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 218.487 1.02742 212.656
    1127 no value nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] 239.219 1.02741 232.837
    1128 SIX1 homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] 221.286 1.02733 215.399
    1129 SIX2 homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] 221.285 1.02732 215.401
    1130 PA2G4 proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] 215.4
    1131 no value vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] 218.484 1.02731 212.675

    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/