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 Network Comparison Type Hugo Value Type description Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 2012 to 2061 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    252 EIF4G1 Ranked eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] High confidence 1.11689 237.292 212.457
    NFYB Rooted nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 1.13099 51.6736 58.4422
    PASK Squared pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 1.3052 69165 52991.7
    RRAGA Rooted ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 1.05706 86.7994 91.752
    RRAS Squared ras-related protein r-ras (p23). [swissprot;acc:p10301] 1.09142 50409.8 46187.4
    253 ABL1 Measured proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] High confidence 1.22477 6417.18 7859.59
    ATP2C1 Rooted calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Low confidence 1.05702 66.0401 69.8058
    BCL6 Squared b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] High confidence 1.3052 69165 52991.7
    FBP2 Measured fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Low confidence 1.06188 8223.39 8732.25
    MXD1 Ranked mad protein (max dimerizer). [swissprot;acc:q05195] High confidence 1.11583 228 204.333
    NOX4 nadph oxidase 4. [refseq;acc:nm_016931] Low confidence 1.04665 210.413 201.035
    RRAS2 Squared ras-related protein r-ras2 (ras-like protein tc21) (teratocarcinoma oncogene). [swissprot;acc:p17082] 1.09133 50402.7 46184.6
    SRP9 Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 1.12817 53.5956 60.465
    254 ARF5 Squared adp-ribosylation factor 5. [swissprot;acc:p26437] Low confidence 1.09133 59478 54500.5
    FYN Measured proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] High confidence 1.22477 6417.18 7859.6
    NOX3 Ranked nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Low confidence 1.04665 210.414 201.035
    SEL1L2 Measured dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] 1.06179 8219.97 8727.87
    SF3B2 Rooted splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 1.05682 70.5903 74.601
    SNAI2 Squared zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] High confidence 1.3052 69165 52991.7
    SRP9 Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1.12756 53.607 60.4452
    STT3B Ranked source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 1.11569 200.691 179.88
    255 CASK Rooted peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Low confidence 1.05667 67.7782 71.6191
    CTBP1 Squared c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] High confidence 1.30503 69123.3 52967
    FGR Measured proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 1.22477 6417.18 7859.6
    GYS1 Squared glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Low confidence 1.09129 53312.7 48853.1
    NOX1 Ranked nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] 1.04665 210.413 201.035
    RRM2 Rooted ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] High confidence 1.12694 62.9007 70.8854
    SEL1L Measured sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] Low confidence 1.06179 8219.95 8727.84
    STT3A Ranked oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence 1.11569 200.691 179.88
    256 no value Squared formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 1.303 15465.1 20151
    CEBPZ Rooted ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 1.12665 48.0045 54.0843
    DDX10 Squared probable atp-dependent rna helicase ddx10 (dead-box protein 10). [swissprot;acc:q13206] Low confidence 1.09119 50792.6 46547.8
    FBP1 Measured fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 1.06171 8216.87 8723.91
    GRAP2 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] High confidence 1.22476 6417.19 7859.51
    MXI1 Ranked max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 1.11569 227.999 204.357
    SIM1 Rooted single-minded homolog 1. [swissprot;acc:p81133] Low confidence 1.05667 67.7782 71.6191
    STT3A Ranked oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 1.04648 199.376 190.521
    257 no value Squared huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] High confidence 1.30229 15482.3 20162.4
    Rooted cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 1.05665 68.3669 72.2396
    COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] High confidence 1.12591 51.6125 45.8409
    CUTL1 Measured ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 1.22452 6417.31 7858.12
    DDOST Ranked 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] 1.11569 200.691 179.88
    GYS2 Squared glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Low confidence 1.09077 53244.4 48813.4
    SYNJ1 Measured synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] 1.06157 8082.34 8579.93
    TPM3 Ranked tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] 1.04632 201.316 192.404
    258 AKR7A3 Measured aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 1.06154 9249.74 9818.95
    CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] High confidence 1.22449 6417.33 7857.93
    HIP1 Squared huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 1.29799 76438 58889.7
    MXD4 Ranked max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 1.11564 227.999 204.366
    PSD3 Squared adp-ribosylation factor guanine nucleotide factor 6; hepatocellular carcinoma-associated antigen 67. [refseq;acc:nm_015310] Low confidence 1.09045 50448.8 46264.1

    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/