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 red Interaction Map Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 1508 to 1557 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] 1902 LBR 191.411 1.01034 193.39
    lamin b1. [swissprot;acc:p20700] 2036 LMNB1 218.919 1.00865 220.813
    lamin b2. [swissprot;acc:q03252] 2723 no value 219.323 1.00041 219.413
    laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 471 LAMC1 248.152 1.07686 267.226
    lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] 1869 LANCL2 220.107 1.01082 217.75
    langerhans cell specific c-type lectin. [refseq;acc:nm_015717] 3046 CD207 0.00001 1 0.00001
    lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] 1870 LANCL1 220.107 1.01082 217.75
    lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214] 2529 LRRC1 221.776 1.00229 222.283
    large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] 2293 no value 200.158 1.00527 201.213
    late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5] 3044 0.00001 1 0.00001
    lats homolog 1. [refseq;acc:nm_004690] 2057 LATS1 218.79 1.00834 216.981
    lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] 2053 LATS2
    lbp-9. [refseq;acc:nm_014553] 1193 TFCP2L1 220.742 1.02558 215.237
    leng5 protein. [refseq;acc:nm_024075] 2260 TSEN34 221.599 1.00566 220.351
    lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 2693 MIP 188.193 1.00077 188.049
    leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] 3017 LRRFIP1 0.00001 1 0.00001
    leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309] 3153 LRRFIP2
    leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 470 LRRC3 248.152 1.07686 267.226
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 2677 SHOC2 144.412 1.00098 144.553
    leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 468 LRRC15 248.152 1.07686 267.226
    leucyl-trna synthetase. [refseq;acc:nm_020117] 1735 LARS 218.99 1.01296 216.189
    leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] 798 SERPINB1 224.244 1.04578 234.511
    leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] 2391 LTA4H 214.966 1.00388 215.799
    lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 1628 FAIM2 217.446 1.01515 214.2
    ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 272 LGTN 241.373 1.10763 267.352
    likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [refseq;acc:nm_173535] 2898 CLEC4F 0.00001 1 0.00001
    likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 231 SHCBP1 239.336 1.11927 267.881
    likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 2250 CSTF2T 164.064 1.00606 165.058
    likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 1283 CYP4X1 218.368 1.02414 213.22
    lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] 1260 LIMS2 219.354 1.02437 224.7
    lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 1897 no value 199.883 1.01035 197.835
    lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] 1896 LDB2
    lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] 2107 LMO7 216.23 1.00727 217.801
    lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 233 CSRP3 239.32 1.11918 267.842
    lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] 2609 LMX1A 215.497 1.0014 215.799
    lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663] 2611 LMX1B
    lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] 1983 PDLIM5 219.25 1.00955 217.175
    lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] 1899 LHX3 199.884 1.01035 197.837
    lim/homeobox protein lhx4. [swissprot;acc:q969g2] 1898 LHX4 199.881 197.833
    limb region 1 protein; limb region 1. [refseq;acc:nm_022458] 2469 LMBR1 235.812 1.00308 235.088
    limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 1482 LSAMP 224.354 1.0191 220.15
    limkain b1. [refseq;acc:nm_019081] 703 KIAA0430 220.438 1.05413 209.118
    limkain beta 2. [refseq;acc:nm_025140] 2096 CCDC92 217.723 1.00756 216.089
    lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] 1987 LIN7A 225.022 1.00952 222.9
    lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] 2001 LIN7B 225.02 1.00929 222.948
    lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] 2027 LIN7C 225.015 1.00885 223.041
    lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182] 2582 DBT 213.422 1.00154 213.75
    lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] 1738 LIPT1 206.595 1.01289 209.258
    lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] 2465 LMBR1L 235.812 1.00308 235.088
    lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] 1347 LIAS 204.961 1.02223 209.517

    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/