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 description Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 475 to 524 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    475 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] KCNA1 226.727 210.816 1.07547
    476 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] KCNA4 226.681 210.814 1.07527
    477 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] NIP7 251.926 234.547 1.0741
    478 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] BRF1 228.051 212.321 1.07409
    479 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] NOLA1
    480 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] NETO2 237.109 254.667 1.07405
    481 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] NETO1
    482 heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] HNRNPU
    483 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] RUNX2
    484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] HNRPUL1
    485 60s ribosomal protein l18. [swissprot;acc:q07020] RPL18
    486 mct-1 protein. [refseq;acc:nm_014060] MCTS1 226.313 243.03 1.07387
    487 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] MRPL22
    488 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] SART1 225.026 209.798 1.07258
    489 protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] PPM1B 231.276 215.627 1.07257
    490 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] ARHGEF7 220.183 236.015 1.0719
    491 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] GTPBP4 251.83 234.951 1.07184
    492 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] PAK2 220.171 235.979 1.0718
    493 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] COG5 220.172 235.98
    494 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] PAK1
    495 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] PAK3 220.171 235.979
    496 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] PPAN-P2RY11 250.938 234.134 1.07177
    497 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] EBNA1BP2 251.344 234.514
    498 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] ARHGEF6 220.161 235.95 1.07172
    499 triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] TPI1 231.496 248.048 1.0715
    500 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] ING2 224.662 240.673 1.07127
    501 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] CYC1 238.704 255.68 1.07112
    502 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] ARHGAP26
    503 senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] RGN
    504 oligophrenin 1. [swissprot;acc:o60890] OPHN1
    505 ad24 protein. [refseq;acc:nm_022451] NOC3L 251.334 234.672 1.071
    506 inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] ING1 224.535 240.476
    507 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] WDR12 251.299 234.729 1.07059
    508 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 177.698 190.24 1.07058
    509 carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 190.239 1.07057
    510 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 177.699 190.24
    511 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] NOL1 250.053 233.725 1.06986
    512 block of proliferation 1. [swissprot;acc:q14137] BOP1 250.794 234.433 1.06979
    513 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] DVL1 218.596 204.344 1.06975
    514 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] DVL2 218.613 204.382 1.06963
    515 pescadillo homolog 1. [swissprot;acc:o00541] PES1 251.297 234.941 1.06962
    516 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] LSM8 228.255 213.422 1.0695
    517 metaxin 2. [swissprot;acc:o75431] MTX2 219.537 234.793 1.06949
    518 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] GNL3 250.858 234.563 1.06947
    519 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 218.702 204.582 1.06902
    520 sqv-7-like protein (fragment). [sptrembl;acc:o95454] SLC35D2 214.754 229.565 1.06897
    521 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] EXOSC4 215.237 230.07 1.06891
    522 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 222.893 208.523
    523 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] EXOSC2 215.237 230.07
    524 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] EXOSC3

    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/