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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2358 to 2407 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    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] Divided Low confidence 211.788 218.216 1.03035
    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] Subtracted 204.056 198.046 6.01
    RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Divided 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
    HRBL hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Subtracted High confidence 217.67 230.596 12.926
    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 6.003
    RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Divided High confidence 216.72 230.439 1.0633
    592 C16orf35 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Subtracted 217.67 230.596 12.926
    ERGIC2 cda14. [refseq;acc:nm_016570] Divided Low confidence 211.525 205.3 1.03032
    NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Subtracted 204.073 198.07 6.003
    PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Divided High confidence 91.63 97.4011 1.06298
    593 ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Subtracted Low confidence 204.856 198.854 6.002
    DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Divided High confidence 232.118 218.406 1.06278
    HTATSF1 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Subtracted 217.67 230.596 12.926
    NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Divided Low confidence 204.074 198.071 1.03031
    594 ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Subtracted 204.843 198.851 5.992
    CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Divided High confidence 223.282 210.136 1.06256
    CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Subtracted 207.26 194.346 12.914
    NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Divided Low confidence 204.073 198.07 1.03031
    595 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Subtracted High confidence 207.26 194.346 12.914
    ABTB1 ankyrin repeat and btb (poz) domain containing 1 isoform 1; elongation factor 1a binding protein. [refseq;acc:nm_032548] Divided Low confidence 205.485 199.453 1.03024
    BUD31 g10 protein homolog (edg-2). [swissprot;acc:p41223] Subtracted 201.67 195.729 5.941
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] Divided High confidence 212.2 199.849 1.0618
    596 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Subtracted 207.26 194.346 12.914
    CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Low confidence 216.618 210.69 5.928
    RBX1 ring-box 1; ring box protein 1; regulator of cullins 1; ring finger protein; zyp protein. [refseq;acc:nm_014248] Divided 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
    DDX17 probable rna-dependent helicase p72 (dead-box protein p72) (dead-box protein 17). [swissprot;acc:q92841] Subtracted 204.837 198.913 5.924
    HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] High confidence 207.26 194.346 12.914
    VAV2 vav-2 protein. [swissprot;acc:p52735] Divided 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
    DDX5 probable rna-dependent helicase p68 (dead-box protein p68) (dead-box protein 5). [swissprot;acc:p17844] Subtracted 204.832 198.916 5.916
    GRAP2 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] High confidence 207.261 194.347 12.914
    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] Divided 248.463 234.095 1.06138
    CRKL crk-like protein. [swissprot;acc:p46109] Subtracted 207.26 194.346 12.914
    JARID2 jumonji protein. [swissprot;acc:q92833] Low confidence 207.726 201.813 5.913
    SFRS3 splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Divided 208.383 202.291 1.03012
    600 ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Subtracted High confidence 207.26 194.346 12.914
    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] Divided 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
    NEUROG2 neurogenin 2 (fragment). [swissprot;acc:q9h2a3] Subtracted 216.554 210.642 5.912
    601 CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Divided 208.67 202.603 1.02995
    FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Subtracted High confidence 207.26 194.346 12.914
    NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Low confidence 216.554 210.642 5.912
    VPS39 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Divided High confidence 206.274 218.792 1.06069
    602 FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Subtracted 207.26 194.346 12.914
    MAP4 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Divided 206.274 218.792 1.06069
    NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted Low confidence 216.552 210.641 5.911

    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/