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 Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2430 to 2479 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640] 3198 DCUN1D1 0.00001 0.00001 1
    rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] 1624 PDCD11 230.643 227.194 1.01518
    runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196] 2877 RUNX1 0.00001 0.00001 1
    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] 483 RUNX2 237.109 254.667 1.07405
    runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761] 3208 RUNX3 0.00001 0.00001 1
    ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] 1759 RUVBL1 219.37 222.086 1.01238
    ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] 2204 RUVBL2 219.377 220.8 1.00649
    rw1 protein (fragment). [swissprot;acc:q92545] 838 TMEM131 231.734 222.222 1.0428
    rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] 3073 RWDD1 0.00001 0.00001 1
    s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] 2647 MAT1A 212.496 212.25 1.00116
    s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 2555 MAT2A 212.953 212.572 1.00179
    s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] 208 SKP1A 285.684 252.234 1.13261
    saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 477 NIP7 251.926 234.547 1.0741
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 148 UNC84A 296.677 247.559 1.19841
    sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] 1387 SALL1 218.47 213.875 1.02148
    sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] 1377 SALL2 218.471 213.876
    sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] 1378 SALL3 218.47
    sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 1388 SALL4 218.471
    salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162] 2716 PRB4 216.018 215.903 1.00053
    sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3] 3124 SAMHD1 0.00001 0.00001 1
    sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] 1176 SGCZ 218.186 212.672 1.02593
    schwannomin interacting protein 1. [refseq;acc:nm_014575] 2900 SCHIP1 0.00001 0.00001 1
    scratch; scratch 1. [refseq;acc:nm_031309] 1873 no value 210.55 208.305 1.01078
    scribble. [refseq;acc:nm_015356] 2528 SCRIB 221.782 222.291 1.0023
    scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] 1575 SCYL1 222.585 218.982 1.01645
    sec13-related protein. [swissprot;acc:p55735] 1133 SEC13 218.484 212.675 1.02731
    sec23-interacting protein p125; phospholipase. [refseq;acc:nm_007190] 3097 SEC23IP 0.00001 0.00001 1
    secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 1644 no value 217.256 214.149 1.01451
    secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] 1646 SMOC2
    secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 2453 SCAMP1 204.688 205.332 1.00315
    secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 2451 SCAMP2 205.333
    secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] 2452 SCAMP3
    secretory pathway component sec31b-1. [refseq;acc:nm_015490] 1143 SEC31B 218.484 212.675 1.02731
    sedlin. [swissprot;acc:o14582] 565 ZNF547 129.219 121.261 1.06563
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 513 DVL1 218.596 204.344 1.06975
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 514 DVL2 218.613 204.382 1.06963
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 519 DVL3 218.702 204.582 1.06902
    selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] 543 SEPHS1 222.156 208.201 1.06703
    selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 540 SEPHS2
    semaphorin 6b precursor (semaphorin z) (sema z). [swissprot;acc:q9h3t3] 2832 SEMA6B 0.00001 0.00001 1
    semaphorin 6c precursor (semaphorin y) (sema y). [swissprot;acc:q9h3t2] 2933 SEMA6C
    semaphorin 6d isoform 3 precursor. [refseq;acc:nm_153617] 2964 SEMA6D
    senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 503 RGN 238.704 255.68 1.07112
    sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] 2843 SENP8 0.00001 0.00001 1
    seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] 1517 FAP 213.267 209.511 1.01793
    septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 909 SEPT1 142.077 136.846 1.03823
    septin 10 isoform 1. [refseq;acc:nm_144710] 737 SEPT10 125.526 119.402 1.05129
    septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 829 SEPT4 135.844 130.259 1.04288
    septin 6. [swissprot;acc:q14141] 744 SEPT6 126.604 120.463 1.05098
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 743 SEPT7 126.215 120.078 1.05111

    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/