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 2125 to 2174 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    266 proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK Divided Rooted 66.1064 74.1074 1.12103
    ribosomal protein l10-like protein. [refseq;acc:nm_080746] RPL10L Subtracted Ranked 243.12 266.662 23.542
    solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] SLC4A1AP Measured 11222.2 9948.93 1273.27
    transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] SIN3A Divided Ranked 241.07 267.88 1.11121
    267 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] no value Subtracted 243.12 266.661 23.541
    cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] CKS2 Measured 11222.2 9948.93 1273.27
    density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] DENR Divided Ranked 241.07 267.88 1.11121
    estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] no value Subtracted Squared 59334.6 68040.1 8705.5
    leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] LRRC3 Divided 26157.6 20236.2 1.29261
    ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] RALGDS Measured 14021.4 11523 1.21682
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Subtracted Rooted 61.2893 70.3856 9.0963
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] ABL2 Divided 66.1064 74.1073 1.12103
    268 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] CTNNAL1 Subtracted Measured 11222.2 9948.93 1273.27
    cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] CPSF2 Divided 24473.9 20127.8 1.21593
    eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] EIF5 Ranked 271.016 244.167 1.10996
    laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] LAMC1 Squared 26157.6 20236.2 1.29261
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Subtracted Rooted 61.2893 70.3856 9.0963
    protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] PRMT3 Ranked 241.625 265.136 23.511
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] no value Divided Rooted 66.1064 74.1074 1.12103
    sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] SH3GL2 Subtracted Squared 35533.9 44227 8693.1
    269 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] no value Ranked 241.625 265.136 23.511
    armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] ARMET Squared 35508.7 44191.4 8682.7
    cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] PCYT1A Divided Ranked 241.373 267.352 1.10763
    crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] BCAR1 Subtracted Measured 4808.79 6074.21 1265.42
    dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] DDOST Rooted 61.2893 70.3856 9.0963
    thymic stromal co-transporter. [refseq;acc:nm_033051] SLC46A2 Divided Squared 26157.6 20236.2 1.29261
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK Rooted 66.1064 74.1074 1.12103
    u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] LSM8 Measured 4590.18 5575.52 1.21466
    270 40s ribosomal protein s3. [swissprot;acc:p23396] RPS3 Subtracted Ranked 241.612 265.119 23.507
    crk-like protein. [swissprot;acc:p46109] CRKL Divided Rooted 66.1064 74.1074 1.12103
    fad synthetase. [refseq;acc:nm_025207] FLAD1 Ranked 241.373 267.352 1.10763
    fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] FIP1L1 Measured 23640.2 19479.8 1.21358
    histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] HDC Subtracted Squared 35508.6 44191.3 8682.7
    t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] CCT4 Measured 4810.22 6075.04 1264.82
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP Rooted 48.0515 39.0445 9.007
    transcription factor iib. [refseq;acc:nm_013242] C16orf80 Divided Squared 64739.9 50300.6 1.28706
    271 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] no value Ranked 241.373 267.352 1.10763
    chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] CHRAC1 Measured 2554.89 3093.78 1.21092
    coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] COPB1 Subtracted Squared 53774.6 45105.5 8669.1
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 Rooted 62.762 53.7761 8.9859
    enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] NEDD9 Measured 4812.01 6076.09 1264.08
    protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] SEC61G Ranked 243.072 266.559 23.487
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 Divided Rooted 66.1064 74.1073 1.12103
    splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] SFRS8 Squared 64739.9 50300.6 1.28706
    272 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] FDX1 36563.7 46971.1 1.28464
    crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] BCAR1 Subtracted Rooted 57.4432 66.3307 8.8875
    histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] HAT1 Divided Measured 3858.52 4669.27 1.21012
    ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] LGTN Ranked 241.373 267.352 1.10763
    mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] MRPL17 Subtracted 242.83 266.248 23.418
    nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] NDUFA12 Measured 1991.03 3221.38 1230.35

    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/