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 [...,...].
    Gene Rank Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2101 to 2150 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    526 AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Measured 10639.9 12117.4 1.13886
    ETFB electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Squared 31189.6 37352.8 1.1976
    RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Ranked 250.538 234.401 1.06884
    SEPT6 septin 6. [swissprot;acc:q14141] Rooted 113.169 123.23 1.0889
    527 DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Ranked 248.56 232.579 1.06871
    DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 166.771 1.08865
    LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Squared 18011.9 21552.8 1.19659
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Measured 4775.11 5438.18 1.13886
    528 AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 10635.3 12111.4 1.13879
    PPP2R1A serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Squared 10606 8868.81 1.19588
    WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Rooted 66.941 72.7546 1.08685
    YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Ranked 222.146 237.393 1.06864
    529 DDX18 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 251.653 235.506 1.06856
    NOL5A nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Rooted 50.3239 54.6658 1.08628
    SLC5A6 sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Squared 28990.9 34656.4 1.19542
    TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Measured 8600.02 9792.49 1.13866
    530 LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Ranked 227.483 212.994 1.06803
    MGLL monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Squared 27179.5 32490.8 1.19542
    PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Measured 8600.02 9792.49 1.13866
    RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Rooted 50.6537 46.6413 1.08603
    531 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
    GTF2B transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Measured 4651.88 5296.78 1.13863
    PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Ranked 223.356 209.149 1.06793
    SLC5A8 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Squared 28980.7 34643.6 1.1954
    532 PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] 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

    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/