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.
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    VALUE = ""

    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 green network_comparison
    Results: HTML CSV LaTeX Showing element 101 to 150 of 321 in total
    Hugo  : no value
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		red
    		green
    		network_comparison
    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] 227.596 219.017 1.03917
    888 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
    898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 229.171 238.048 1.03874
    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] 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
    908 tax interaction protein 1. [refseq;acc:nm_014604] 223.906 215.653 1.03827
    910 uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 217.168 209.207 1.03805
    911 ero1-like. [refseq;acc:nm_014584]
    927 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 217.942 210.139 1.03713
    935 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] 232.473 224.372 1.03611
    936 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
    946 histone h4. [swissprot;acc:p02304] 227.765 219.902 1.03576
    949 huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 217.253 209.826 1.0354
    959 guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] 237.558 229.677 1.03431
    978 prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] 228.953 221.421 1.03402
    996 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 219.656 212.547 1.03345
    1000 sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 225.167 217.922 1.03325
    1004 sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 238.725 231.059 1.03318
    1009 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 229.116 221.823 1.03288
    1038 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 186.741 181.041 1.03148
    1042 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 186.799 181.127 1.03132
    1049 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 211.449 217.998 1.03097
    1051 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
    1054 60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 217.263 1.03082
    1059 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 228.105 221.293 1.03078
    1063 zinc finger imprinted 2. [swissprot;acc:q9nzv7] 269.96 278.232 1.03064
    1071 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 231.277 238.356 1.03061
    1086 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 236.679 243.679 1.02958
    1087 zinc finger protein 277. [swissprot;acc:q9nrm2]
    1090 similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 226.218 232.88 1.02945
    1091 block 23. [sptrembl;acc:q8nhw5] 226.205 232.858 1.02941
    1102 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 229.442 235.974 1.02847
    1111 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 217.99 212.123 1.02766
    1125 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 204.404 210.022 1.02748
    1127 nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] 239.219 232.837 1.02741
    1131 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] 218.484 212.675 1.02731
    1148 ubiquitin. [swissprot;acc:p02248] 209.061 203.518 1.02724
    1161 kappa b-ras 1. [refseq;acc:nm_020345] 220.758 215.097 1.02632
    1170 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] 219.399 213.784 1.02626
    1172 transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 219.375 213.767 1.02623
    1186 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 218.402 212.904 1.02582
    1189 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 209.649 204.406 1.02565
    1206 integral membrane protein cii-3b. [sptrembl;acc:o75609] 207.646 212.891 1.02526
    1208 signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 224.878 219.342 1.02524
    1214 kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 214.364 219.759 1.02517
    1233 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] 212.724 207.637 1.0245
    1235 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 219.356 224.723 1.02447
    1236 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 219.354 224.699 1.02437
    1237 keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062]

    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/