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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2125 to 2174 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    532 PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Squared 28967 34626.4 1.19537
    SEPT4 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] Rooted 107.961 117.197 1.08555
    ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] Ranked 250.942 235.004 1.06782
    ZNHIT3 thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Measured 4651.88 5296.78 1.13863
    533 MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Rooted 50.8036 46.8198 1.08509
    NHP2L1 nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Measured 4651.88 5296.78 1.13863
    SLC45A2 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Ranked 250.942 235.004 1.06782
    SLC5A5 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Squared 28937.1 34588.8 1.19531
    534 no value guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Ranked 250.942 235.004 1.06782
    DHDDS dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] Squared 27034.1 32301.8 1.19485
    NUFIP1 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Measured 4651.88 5296.78 1.13863
    RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] Rooted 50.8036 46.8198 1.08509
    535 MPP3 maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Squared 37147.5 44372.1 1.19448
    POLR2H dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Ranked 236.662 252.708 1.0678
    RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Rooted 50.8041 46.8218 1.08505
    SSR4 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Measured 10603.5 12069.5 1.13826
    536 CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985]
    HOXA10 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Rooted 66.0815 71.6562 1.08436
    ITM2B integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Squared 28657.6 34208.6 1.1937
    SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Ranked 242.531 227.136 1.06778
    537 no value succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Measured 10603.5 12069.5 1.13826
    DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Ranked 229.803 215.301 1.06736
    HOXB9 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Rooted 66.0817 71.6545 1.08433
    ITM2C integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Squared 28657.6 34208.6 1.1937
    538 HOXA9 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Rooted 66.0817 71.6543 1.08433
    ITM2A integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Squared 28657.6 34208.6 1.1937
    POLR2L dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] Ranked 237.627 253.604 1.06724
    PTPRB protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Measured 10603.5 12069.4 1.13825
    539 HOXC9 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Rooted 66.0818 71.6537 1.08432
    MEMO1P protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Ranked 236.964 252.86 1.06708
    PRSS16 thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Measured 10603.5 12069.4 1.13825
    WRNIP1 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Squared 20613.1 24595.9 1.19322
    540 ASL argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 26048.6 31057.4 1.19229
    CCDC47 gk001 protein. [refseq;acc:nm_020198] Measured 10603.5 12069.4 1.13825
    GABRG3 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Rooted 66.082 71.6526 1.0843
    SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Ranked 222.156 208.201 1.06703
    541 CLSTN2 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Measured 10600.3 12065.2 1.13819
    COPB1 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Squared 53774.6 45105.5 1.1922
    FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Rooted 66.082 71.6526 1.0843
    MICAL2 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Ranked 222.156 208.201 1.06703
    542 AKT1 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Measured 3889.27 4426.74 1.13819
    GABRG1 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Rooted 66.082 71.6526 1.0843
    INPP4B inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Ranked 222.156 208.201 1.06703
    MAT1A s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Squared 26084.2 31084.3 1.19169
    543 CLSTN3 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Measured 10599.9 12064.7 1.13819
    CNDP1 glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Squared 26612.5 31709 1.19151
    GABRA2 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Rooted 66.082 71.6525 1.0843
    SEPHS1 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Ranked 222.156 208.201 1.06703
    544 AKT3 rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Measured 3889.27 4426.74 1.13819
    GABRA6 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Rooted 66.082 71.6525 1.0843

    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/