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 5591 to 5640 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    Hugo
    description
    Network Comparison Type
    Interaction Map
    red
    green
    network_comparison
    1398 EYA4 eyes absent homolog 4. [swissprot;acc:o95677] Divided High confidence 218.449 213.864 1.02144
    WDR26 wd repeat domain 26. [refseq;acc:nm_025160] Subtracted 213.351 217.74 4.389
    1399 BRUNOL4 bruno-like 4, rna binding protein; rna-binding protein brunol-5; cug-bp and etr-3 like factor 4. [refseq;acc:nm_020180] Low confidence 202.785 198.472 4.313
    EYA2 eyes absent homolog 2. [swissprot;acc:o00167] Divided High confidence 218.417 213.848 1.02137
    MPP6 maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Subtracted 228.469 232.855 4.386
    SPOP speckle-type poz protein. [swissprot;acc:o43791] Divided Low confidence 201.397 197.08 1.0219
    1400 ANXA11 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 203.717 199.354 1.02189
    ATF7 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] High confidence 218.667 214.118 1.02125
    CAPZA3 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] Subtracted Low confidence 201.426 197.115 4.311
    PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] High confidence 170.28 165.898 4.382
    1401 ATF2 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Divided 218.657 214.11 1.02124
    NFKBIA nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963] Low confidence 202.066 197.737 1.02189
    NR6A1 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Subtracted High confidence 212.833 208.456 4.377
    SYT14 synaptotagmin xiv. [refseq;acc:nm_153262] Low confidence 203.719 199.408 4.311
    1402 ARG2 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Divided 201.12 196.811 1.02189
    MCC colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] High confidence 209.682 205.329 1.0212
    Subtracted 4.353
    PDE9A high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083] Low confidence 187.917 183.608 4.309
    1403 CAPZA3 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] Divided 201.426 197.115 1.02187
    CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Subtracted High confidence 110.2 114.552 4.352
    ECHS1 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Divided 184.656 180.823 1.0212
    KIAA0664 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] Subtracted Low confidence 200.723 196.414 4.309
    1404 ABCE1 atp-binding cassette sub-family e member 1 (rnase l inhibitor) (ribonuclease 4 inhibitor) (rns4i) (huhp68). [swissprot;acc:q96b10] Divided 202.268 197.939 1.02187
    KRR1 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Subtracted High confidence 242.181 237.834 4.347
    SF3B4 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Divided 232.752 237.65 1.02104
    SLC36A1 solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483] Subtracted Low confidence 187.917 183.608 4.309
    1405 ARG2 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] 201.12 196.811
    CYR61 cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [swissprot;acc:o00622] Divided 208.227 203.771 1.02187
    EIF3C eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] High confidence 245.532 240.483 1.021
    EVI5L similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Subtracted 218.829 214.493 4.336
    1406 AGPAT2 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Low confidence 198.322 194.014 4.308
    EVI5 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] High confidence 218.829 214.493 4.336
    MPPED2 fetal brain protein 239 (239fb). [swissprot;acc:q15777] Divided Low confidence 204.115 199.746 1.02187
    NR6A1 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] High confidence 212.833 208.456 1.021
    1407 F11R junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] Subtracted Low confidence 200.065 195.758 4.307
    PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Divided 197.603 193.375 1.02186
    WDFY1 wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] High confidence 206.104 210.424 1.02096
    Subtracted 4.32
    1408 no value 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Low confidence 198.342 194.038 4.304
    EARS2 glutamyl trna synthetase. [sptrembl;acc:o14563] Divided 196.216 192.019 1.02186
    STIM1 stromal interaction molecule 1 precursor. [swissprot;acc:q13586] High confidence 206.102 210.42 1.02095
    Subtracted 4.318
    1409 ASNS asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Low confidence 187.8 183.496 4.304
    MED30 trap/mediator complex component trap25. [refseq;acc:nm_080651] Divided High confidence 206.102 210.42 1.02095
    Subtracted 4.318
    NFIL3 nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] Divided Low confidence 195.821 191.636 1.02184
    1410 PAK4 serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] Subtracted High confidence 206.102 210.42 4.318
    RAB13 ras-related protein rab-13. [swissprot;acc:p51153] Low confidence 200.618 196.316 4.302
    RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Divided 199.829 195.558 1.02184
    WDFY2 wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] High confidence 206.1 210.417 1.02095

    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/