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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1930 to 1979 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    483 BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Subtracted High confidence 228.051 15.73 212.321
    RUNX2 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Divided 237.109 1.07405 254.667
    TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Subtracted Low confidence 204.65 6.564 198.086
    484 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Divided 203.821 1.0331 197.291
    HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] High confidence 237.109 1.07405 254.667
    NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Subtracted 228.051 15.73 212.321
    SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Low confidence 203.822 6.563 197.259
    485 BRPF1 tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Divided 205.109 1.03303 198.551
    Subtracted 6.558
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] High confidence 231.276 15.649 215.627
    RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] Divided 237.109 1.07405 254.667
    486 CXorf9 chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] Low confidence 204.331 1.03301 211.075
    EEF1B2 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Subtracted 206.154 6.558 199.596
    EIF6 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] High confidence 248.866 15.579 233.287
    MCTS1 mct-1 protein. [refseq;acc:nm_014060] Divided 226.313 1.07387 243.03
    487 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Subtracted Low confidence 194.237 6.548 187.689
    C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Divided 206.763 1.03289 200.18
    MDH2 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Subtracted High confidence 238.529 15.57 254.099
    MRPL22 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Divided 226.313 1.07387 243.03
    488 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Subtracted 82.5916 15.4632 98.0548
    PCNA proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Low confidence 207.84 6.543 201.297
    SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Divided High confidence 225.026 1.07258 209.798
    TMOD4 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Low confidence 209.136 1.03288 202.478
    489 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Subtracted High confidence 82.5916 15.4632 98.0548
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided 231.276 1.07257 215.627
    TMOD3 ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Low confidence 209.136 1.03288 202.478
    USP22 ubiquitin carboxyl-terminal hydrolase 22 (ec 3.1.2.15) (ubiquitin thiolesterase 22) (ubiquitin-specific processing protease 22) (deubiquitinating enzyme 22) (fragment). [swissprot;acc:q9upt9] Subtracted 207.407 6.538 200.869
    490 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Divided High confidence 220.183 1.0719 236.015
    FUCA2 fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] Subtracted Low confidence 202.311 6.533 195.778
    SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] High confidence 242.531 15.395 227.136
    TMOD1 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Divided Low confidence 209.136 1.03288 202.478
    491 no value rna-binding protein. [refseq;acc:nm_019027] Subtracted 203.821 6.532 197.289
    GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Divided High confidence 251.83 1.07184 234.951
    PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 150.959 15.392 166.351
    SNX9 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Divided Low confidence 209.136 1.03288 202.478
    492 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Subtracted 203.821 6.53 197.291
    ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] High confidence 150.982 15.39 166.372
    PAK2 serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Divided 220.171 1.0718 235.979
    TMOD2 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Low confidence 209.136 1.03288 202.478
    493 COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] High confidence 220.172 1.0718 235.98
    FUCA1 tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] Subtracted Low confidence 202.271 6.529 195.742
    TNK2 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Divided 209.136 1.03288 202.478
    ZNRD1 zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Subtracted High confidence 236.751 15.287 252.038
    494 EEF1B2 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Divided Low confidence 206.154 1.03286 199.596
    EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Subtracted 208.004 6.507 201.497
    MTX2 metaxin 2. [swissprot;acc:o75431] High confidence 219.537 15.256 234.793
    PAK1 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Divided 220.172 1.0718 235.98
    495 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Subtracted Low confidence 198.464 6.504 191.96
    LIMD1 lim domains containing 1. [refseq;acc:nm_014240] Divided 203.117 1.03278 196.671
    PAK3 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] High confidence 220.171 1.0718 235.979

    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/