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 description Gene Hugo 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
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    532 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] PRODH2 Squared 28967 34626.4 1.19537
    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] SEPT4 Rooted 107.961 117.197 1.08555
    thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] ZNHIT3 Measured 4651.88 5296.78 1.13863
    zinc finger-like protein 9. [refseq;acc:nm_033414] ZNF622 Ranked 250.942 235.004 1.06782
    533 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] MRPL13 Rooted 50.8036 46.8198 1.08509
    membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] SLC45A2 Ranked 250.942 235.004 1.06782
    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] NHP2L1 Measured 4651.88 5296.78 1.13863
    sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] SLC5A5 Squared 28937.1 34588.8 1.19531
    534 40s ribosomal protein s16. [swissprot;acc:p17008] RPS16 Rooted 50.8036 46.8198 1.08509
    dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] DHDDS Squared 27034.1 32301.8 1.19485
    guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] no value Ranked 250.942 235.004 1.06782
    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] NUFIP1 Measured 4651.88 5296.78 1.13863
    535 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] RPL13A Rooted 50.8041 46.8218 1.08505
    dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] POLR2H Ranked 236.662 252.708 1.0678
    maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] MPP3 Squared 37147.5 44372.1 1.19448
    translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] SSR4 Measured 10603.5 12069.5 1.13826
    536 calsyntenin-1 precursor. [swissprot;acc:o94985] CLSTN1
    homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] HOXA10 Rooted 66.0815 71.6562 1.08436
    integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] ITM2B Squared 28657.6 34208.6 1.1937
    lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] SSB Ranked 242.531 227.136 1.06778
    537 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] HOXB9 Rooted 66.0817 71.6545 1.08433
    integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] ITM2C Squared 28657.6 34208.6 1.1937
    putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] DHX15 Ranked 229.803 215.301 1.06736
    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] no value Measured 10603.5 12069.5 1.13826
    538 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] POLR2L Ranked 237.627 253.604 1.06724
    homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] HOXA9 Rooted 66.0817 71.6543 1.08433
    integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] ITM2A Squared 28657.6 34208.6 1.1937
    protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] PTPRB Measured 10603.5 12069.4 1.13825
    539 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] HOXC9 Rooted 66.0818 71.6537 1.08432
    protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] MEMO1P Ranked 236.964 252.86 1.06708
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] PRSS16 Measured 10603.5 12069.4 1.13825
    werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] WRNIP1 Squared 20613.1 24595.9 1.19322
    540 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] ASL 26048.6 31057.4 1.19229
    gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] GABRG3 Rooted 66.082 71.6526 1.0843
    gk001 protein. [refseq;acc:nm_020198] CCDC47 Measured 10603.5 12069.4 1.13825
    selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] SEPHS2 Ranked 222.156 208.201 1.06703
    541 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] CLSTN2 Measured 10600.3 12065.2 1.13819
    coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] COPB1 Squared 53774.6 45105.5 1.1922
    flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] MICAL2 Ranked 222.156 208.201 1.06703
    forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] FOXG1 Rooted 66.082 71.6526 1.0843
    542 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] GABRG1
    inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] INPP4B Ranked 222.156 208.201 1.06703
    rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] AKT1 Measured 3889.27 4426.74 1.13819
    s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] MAT1A Squared 26084.2 31084.3 1.19169
    543 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] CLSTN3 Measured 10599.9 12064.7 1.13819
    gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] GABRA2 Rooted 66.082 71.6525 1.0843
    glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] CNDP1 Squared 26612.5 31709 1.19151
    selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] SEPHS1 Ranked 222.156 208.201 1.06703
    544 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] GABRA6 Rooted 66.082 71.6525 1.0843
    inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] INPP4A Ranked 222.156 208.201 1.06703

    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/