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 green network_comparison
    Results: HTML CSV LaTeX Showing element 1175 to 1224 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    588 AGPAT4 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Low confidence 191.507 185.859 1.03039
    SBDS shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] High confidence 216.557 230.362 1.06375
    589 no value u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 228.215 214.546 1.06371
    NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Low confidence 204.056 198.046 1.03035
    590 AP2M1 clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] 211.788 218.216
    RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] High confidence 217.215 204.279 1.06333
    591 BUD31 g10 protein homolog (edg-2). [swissprot;acc:p41223] Low confidence 201.67 195.729 1.03035
    RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] High confidence 216.72 230.439 1.0633
    592 ERGIC2 cda14. [refseq;acc:nm_016570] Low confidence 211.525 205.3 1.03032
    PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] High confidence 91.63 97.4011 1.06298
    593 DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 232.118 218.406 1.06278
    NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Low confidence 204.074 198.071 1.03031
    594 CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] High confidence 223.282 210.136 1.06256
    NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Low confidence 204.073 198.07 1.03031
    595 ABTB1 ankyrin repeat and btb (poz) domain containing 1 isoform 1; elongation factor 1a binding protein. [refseq;acc:nm_032548] 205.485 199.453 1.03024
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] High confidence 212.2 199.849 1.0618
    596 RBX1 ring-box 1; ring box protein 1; regulator of cullins 1; ring finger protein; zyp protein. [refseq;acc:nm_014248] Low confidence 205.485 199.453 1.03024
    VAV3 vav-3 protein. [swissprot;acc:q9ukw4] High confidence 212.253 199.908 1.06175
    597 ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Low confidence 204.856 198.854 1.03018
    VAV2 vav-2 protein. [swissprot;acc:p52735] High confidence 212.526 200.212 1.0615
    598 AKT1 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 248.463 234.095 1.06138
    ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Low confidence 204.843 198.851 1.03013
    599 AKT3 rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] High confidence 248.463 234.095 1.06138
    SFRS3 splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Low confidence 208.383 202.291 1.03012
    600 AKT2 rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] High confidence 248.463 234.095 1.06138
    ING3 inhibitor of growth family, member 3. [refseq;acc:nm_019071] Low confidence 210.546 204.42 1.02997
    601 CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 208.67 202.603 1.02995
    VPS39 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] High confidence 206.274 218.792 1.06069
    602 MAP4 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
    SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Low confidence 201.426 195.579 1.0299
    603 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 201.427 195.587 1.02986
    LEF1 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] High confidence 225.829 212.945 1.0605
    604 RPL15 60s ribosomal protein l15. [swissprot;acc:p39030] 217.862 230.978 1.0602
    RPL36 60s ribosomal protein l36. [swissprot;acc:q9y3u8] Low confidence 205.116 211.234 1.02983
    605 DDX17 probable rna-dependent helicase p72 (dead-box protein p72) (dead-box protein 17). [swissprot;acc:q92841] 204.837 198.913 1.02978
    HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] High confidence 247.47 233.441 1.0601
    606 no value dolichyl-p-man:man(5)glcnac(2)-pp-dolichyl mannosyltransferase (ec 2.4.1.-) (dol-p-man dependent alpha(1-3)-mannosyltransferase) (not56-like protein). [swissprot;acc:q92685] Low confidence 200.085 194.301 1.02977
    HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] High confidence 247.47 233.441 1.0601
    607 no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]
    DDX5 probable rna-dependent helicase p68 (dead-box protein p68) (dead-box protein 5). [swissprot;acc:p17844] Low confidence 204.832 198.916 1.02974
    608 no value ba161i19.3 (similar to ribosomal protein l36). [sptrembl;acc:q8wx03] 205.117 211.213 1.02972
    histone h2b. [refseq;acc:nm_175055] High confidence 247.47 233.441 1.0601
    609 histone h2b.s (h2b/s). [swissprot;acc:p57053]
    TP63 tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Low confidence 191.867 186.346 1.02963
    610 no value histone h2b.d (h2b/d). [swissprot;acc:q99877] High confidence 247.47 233.441 1.0601
    TP73 tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Low confidence 191.871 186.351 1.02962
    611 HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] High confidence 247.47 233.441 1.0601
    TP53 cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Low confidence 191.875 186.357 1.02961
    612 HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] High confidence 247.47 233.441 1.0601
    PDIA4 protein disulfide isomerase a4 precursor (ec 5.3.4.1) (protein erp-72) (erp72). [swissprot;acc:p13667] Low confidence 204.388 198.518 1.02957

    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/