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 [...,...].
    Gene description Rank Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2308 to 2357 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    ral-a exchange factor ralgps2. [refseq;acc:nm_152663] 1808 RALGPS2 211.102 208.651 1.01175
    rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788] 3212 RALBP1 0.00001 0.00001 1
    ran binding protein 11. [refseq;acc:nm_016338] 2597 IPO11 212.711 212.401 1.00146
    ran binding protein 3 isoform ranbp3-d; ran-binding protein-3. [refseq;acc:nm_007322] 3202 RANBP3 0.00001 0.00001 1
    ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] 2109 RANBP2 219.032 217.47 1.00718
    ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 2111 no value 219.047 217.511 1.00706
    2113 219.055 217.533 1.007
    ran-gtp binding protein (fragment). [sptrembl;acc:o60518] 1476 RANBP6 218.591 214.457 1.01928
    rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 161 RAP1GAP 249.663 298.263 1.19466
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 137 RASAL2 350 290 1.2069
    ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] 1253 RSU1 219.354 224.7 1.02437
    ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] 1254 G3BP1
    ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] 1255 G3BP2
    ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] 1669 no value 228.496 231.729 1.01415
    ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153] 1672 RAC2
    ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] 1670 RAC3
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 140 RRAGA 59 49 1.20408
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 142 RRAGB
    ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 141 RRAGC
    ras-related protein rab-11a (rab-11) (24kg) (yl8). [swissprot;acc:p24410] 3112 RAB11A 0.00001 0.00001 1
    ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907] 2764 RAB11B
    ras-related protein rab-1a (ypt1-related protein). [swissprot;acc:p11476] 2961 RAB1A
    ras-related protein rab-1b. [swissprot;acc:q9h0u4] 2807 RAB1C
    ras-related protein rab-26. [swissprot;acc:q9ulw5] 423 RAB26 240.287 260.193 1.08284
    ras-related protein rab-2a. [swissprot;acc:p08886] 3110 RAB2A 0.00001 0.00001 1
    ras-related protein rab-37. [swissprot;acc:q96ax2] 422 RAB37 240.287 260.193 1.08284
    ras-related protein ral-a. [swissprot;acc:p11233] 3223 RALA 0.00001 0.00001 1
    ras-related protein ral-b. [swissprot;acc:p11234] 2925 RALB
    rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781] 3205 RB1CC1
    rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [refseq;acc:nm_005444] 2924 RQCD1
    rd protein. [swissprot;acc:p18615] 238 no value 227.357 254.15 1.11785
    receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] 2006 ERBB2 225.019 222.971 1.00919
    receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] 2008 ERBB3 222.969
    receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] 2004 ERBB4
    recessive polycystic kidney disease protein tg737 homolog. [swissprot;acc:q13099] 3201 IFT88 0.00001 0.00001 1
    red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] 2707 ACP1 215.096 215.232 1.00063
    regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] 1972 SEC16B 219.777 217.659 1.00973
    regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 2277 RCC1 191.936 190.909 1.00538
    regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 159 RGS17 249.663 298.263 1.19466
    regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 154 RGS19
    regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] 156 RGS20
    regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [swissprot;acc:q15714] 3114 TSC22D1 0.00001 0.00001 1
    replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] 402 RPA2 207.908 226.218 1.08807
    replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] 401 RPA1
    repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 1352 no value 211.513 206.941 1.02209
    rest corepressor. [refseq;acc:nm_015156] 1976 RCOR1 214.611 212.546 1.00972
    ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 2098 no value 177.515 178.831 1.00741
    reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] 1461 RTN1 207.019 211.077 1.0196
    reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] 1453 RTN4 207.038 211.13 1.01976
    reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] 1466 RTN2 207.022 211.073 1.01957

    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/