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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map red Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 2512 to 2561 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] 2317 PPP6C 194.834 1.00493 195.794
    serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 2018 PPP1CA 127.397 1.00907 128.553
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 1814 PPP1CC 122.3 1.01167 123.727
    serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757] 2908 CHEK1 0.00001 1 0.00001
    serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] 2701 DCLK1 216.539 1.00066 216.682
    serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] 3137 CDKL1 0.00001 1 0.00001
    serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] 2346 NEK1 217.057 1.00448 218.03
    serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] 447 NEK2 224.049 1.07827 207.785
    serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] 2347 NEK3 217.057 1.00448 218.03
    serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] 494 PAK1 220.172 1.0718 235.98
    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] 492 PAK2 220.171 235.979
    serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 495 PAK3
    serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] 1411 PAK4 206.102 1.02095 210.42
    serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286] 1416 PAK7
    serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] 2176 PLK1 218.089 1.00669 216.64
    serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] 1364 ACVR1B 223.885 1.02194 228.797
    serine/threonine-protein kinase receptor r3 precursor (ec 2.7.1.37) (skr3) (activin receptor-like kinase 1) (alk-1) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:p37023] 2952 ACVRL1 0.00001 1 0.00001
    serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] 2089 UTP14A 215.144 1.0078 213.479
    serpin b11. [swissprot;acc:q96p15] 795 no value 224.244 1.04578 234.511
    serpin b12. [swissprot;acc:q96p63] 2413 SERPINB12 218.2 1.00359 218.984
    seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] 2118 SARS 214.632 1.007 213.14
    seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] 2117 SARS2
    sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 1290 SESN1 218.368 1.02414 213.22
    sestrin 2 (hi95). [swissprot;acc:p58004] 1279 SESN2 1.02415 213.219
    sestrin 3. [swissprot;acc:p58005] 1278 SESN3
    set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 417 SETMAR 233.539 1.08417 253.197
    set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105] 3039 SET 0.00001 1 0.00001
    seven in absentia homolog 1. [refseq;acc:nm_003031] 2234 no value 223.608 1.00625 225.005
    seven in absentia homolog 2. [refseq;acc:nm_005067] 2256 SIAH2 223.546 1.00592 224.869
    sex comb on midleg homolog 1. [refseq;acc:nm_012236] 3217 SCMH1 0.00001 1 0.00001
    sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089] 3120 SCML2
    sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] 1684 SRPK1 216.899 1.01407 213.889
    sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] 1682 SRPK2
    sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 1004 no value 238.725 1.03318 231.059
    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] 228 SH2D3C 226.411 1.12036 202.088
    sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] 2794 SH2B1 0.00001 1 0.00001
    sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] 2867 no value
    sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] 2050 SH3BGR 218.79 1.00834 216.981
    sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] 2058 no value
    sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] 2056 SH3BGRL
    sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 1718 SH3GL1 206.251 1.01325 203.553
    sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] 1716 SH3GL2 206.522 1.01327 203.818
    sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 1713 SH3GL3 206.823 1.01329 204.111
    shc transforming protein. [swissprot;acc:p29353] 2125 SHC1 221.248 1.00696 222.788
    short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] 646 SCOC 216.731 1.05914 229.549
    short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 202 TRPC4 201.478 1.13553 228.784
    short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 204 TRPC5 201.515 1.13516 228.752
    shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 363 SHROOM3 231.481 1.09639 211.131
    shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] 588 SBDS 216.557 1.06375 230.362
    signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] 2695 SRP54 215.545 1.00075 215.384

    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/