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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2330 to 2379 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		red
    		green
    		network_comparison
    583 Ranked OPN4 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] 237.28 252.492 1.06411
    Squared AKR7A3 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 23526.4 27879.3 1.18502
    Rooted HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 121.695 131.815 1.08316
    584 Measured GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 6739.82 7644.63 1.13425
    Ranked TLX2 t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] 237.28 252.492 1.06411
    Squared ABHD3 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] 23526.4 27879.3 1.18502
    Rooted SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 104.459 113.143 1.08313
    585 Measured GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 6739.82 7644.63 1.13425
    Ranked TLX1 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] 237.28 252.492 1.06411
    Squared YIPF5 golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] 23526.4 27879.3 1.18502
    Rooted no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 51.5667 55.8498 1.08306
    586 Measured JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 6739.81 7644.62 1.13425
    Ranked HECTD1 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] 237.28 252.492 1.06411
    Squared ABHD1 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] 23526.4 27879.3 1.18502
    Rooted no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 51.5667 55.8498 1.08306
    587 Measured GABRA1 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 6739.83 7644.63 1.13425
    Ranked BARX2 homeobox protein barh-like 2. [swissprot;acc:q9umq3] 237.28 252.492 1.06411
    Squared ALDH6A1 methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] 23526.5 27879.4 1.18502
    Rooted FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 51.7204 56.0156 1.08305
    588 Measured GABRA3 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 6739.83 7644.63 1.13425
    Ranked SBDS shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] 216.557 230.362 1.06375
    Squared HSPE1 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 23526.4 27879.3 1.18502
    Rooted IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 59.7294 64.6872 1.083
    589 Measured NDUFA6 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 6739.85 7644.63 1.13424
    Ranked no value u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 228.215 214.546 1.06371
    Squared RABAC1 rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] 23526.4 27879.3 1.18502
    Rooted no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 59.7294 64.6872 1.083
    590 Measured PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 6739.85 7644.63 1.13424
    Ranked RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 217.215 204.279 1.06333
    Squared REXO2 oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] 23526.4 27879.3 1.18502
    Rooted KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 108.671 100.365 1.08276
    591 Measured HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 6740.5 7644.76 1.13415
    Ranked RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] 216.72 230.439 1.0633
    Squared CHAT choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 23526.5 27879.4 1.18502
    Rooted SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 108.659 100.356 1.08274
    592 Measured HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] 3946.32 4475.47 1.13409
    Ranked PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 91.63 97.4011 1.06298
    Squared KCNAB2 voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] 23526.4 27879.3 1.18502
    Rooted no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 108.659 100.356 1.08274
    593 Measured HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 3946.32 4475.47 1.13409
    Ranked DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 232.118 218.406 1.06278
    Squared AKR7A2 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 23526.4 27879.3 1.18502
    Rooted HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 108.653 100.352 1.08272
    594 Measured no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 3946.32 4475.47 1.13409
    Ranked CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 223.282 210.136 1.06256
    Squared KPNA1 importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] 23517.1 27867.3 1.18498
    Rooted no value transforming protein n-ras. [swissprot;acc:p01111] 108.65 100.35 1.08271
    595 Measured histone h2b. [refseq;acc:nm_175055] 3946.32 4475.47 1.13409
    Ranked VAV1 vav proto-oncogene. [swissprot;acc:p15498] 212.2 199.849 1.0618
    Squared PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 34129.7 40434.8 1.18474

    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/