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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2475 to 2524 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		red
    		green
    		network_comparison
    1238 no value Divided keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 219.354 224.699 1.02437
    UXT Subtracted uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] 226.439 221.26 5.179
    1239 no value Divided keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] 219.354 224.699 1.02437
    STAT4 Subtracted signal transducer and activator of transcription 4. [swissprot;acc:q14765] 222.573 227.751 5.178
    1240 no value Divided keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 219.354 224.7 1.02437
    STAT1 Subtracted signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] 222.574 227.752 5.178
    1241 no value Divided keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] 219.354 224.7 1.02437
    STAT3 Subtracted signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] 222.573 227.75 5.177
    1242 no value Divided keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 219.354 224.7 1.02437
    RALGDS Subtracted ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 162.055 156.884 5.171
    1243 no value Divided keratin associated protein 1.5. [refseq;acc:nm_031957] 219.354 224.699 1.02437
    STAT6 Subtracted signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] 222.569 227.739 5.17
    1244 STARD6 Divided star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 219.354 224.7 1.02437
    TPD52L1 Subtracted tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] 206.774 211.936 5.162
    1245 KRTAP5-8 Divided keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] 219.354 224.699 1.02437
    TPD52 Subtracted tumor protein d52 (n8 protein). [swissprot;acc:p55327] 206.771 211.926 5.155
    1246 no value Divided keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 219.354 224.699 1.02437
    SESN3 Subtracted sestrin 3. [swissprot;acc:p58005] 218.368 213.219 5.149
    1247 SESN2 sestrin 2 (hi95). [swissprot;acc:p58004]
    STARD5 Divided star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] 219.354 224.7 1.02437
    1248 CYP4A11 Subtracted cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 218.368 213.22 5.148
    KRTAP4-4 Divided keratin associated protein 4.4. [refseq;acc:nm_032524] 219.354 224.699 1.02437
    1249 no value alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 224.7
    CYP4F3 Subtracted cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] 218.368 213.22 5.148
    1250 CYP4F8 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]
    LIMS1 Divided pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] 219.354 224.7 1.02437
    1251 CYP4X1 Subtracted likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 218.368 213.22 5.148
    ILK Divided integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] 219.354 224.7 1.02437
    1252 CYP4F12 Subtracted cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 218.368 213.22 5.148
    STARD4 Divided star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] 219.354 224.7 1.02437
    1253 CYP4F2 Subtracted cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 218.368 213.22 5.148
    RSU1 Divided ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] 219.354 224.7 1.02437
    1254 CYP4F11 Subtracted cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 218.368 213.22 5.148
    G3BP1 Divided ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] 219.354 224.7 1.02437
    1255 CYP4A22 Subtracted dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] 218.368 213.22 5.148
    G3BP2 Divided ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] 219.354 224.7 1.02437
    1256 no value keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 224.699
    CYP4B1 Subtracted cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 218.368 213.22 5.148
    1257 ESPNP Divided espin. [refseq;acc:nm_031475] 219.354 224.7 1.02437
    FLOT1 Subtracted flotillin-1. [swissprot;acc:o75955] 218.368 213.22 5.148
    1258 CYP2D6 Divided cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] 219.354 224.7 1.02437
    SESN1 Subtracted sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 218.368 213.22 5.148
    1259 PLEKHC1 Divided pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] 219.354 224.7 1.02437
    STAT5A Subtracted signal transducer and activator of transcription 5a. [swissprot;acc:p42229] 222.546 227.673 5.127
    1260 LIMS2 Divided lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] 219.354 224.7 1.02437
    STAT5B Subtracted signal transducer and activator of transcription 5b. [swissprot;acc:p51692] 222.544 227.667 5.123
    1261 CCT5 t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] 163.24 168.359 5.119
    DRD4 Divided d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] 219.354 224.7 1.02437
    1262 DIMT1L Subtracted probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] 226.347 221.259 5.088
    KRTAP9-8 Divided keratin associated protein 9.2. [refseq;acc:nm_031961] 219.353 224.678 1.02428

    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/