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 [...,...].
    Filtered Rank Gene Hugo description Value Type Network Comparison Type Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 51 to 100 of 3730 in total
    Filtered  : 0
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    51 KPNA2 importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 7168 5102 1.40494
    52 ARIH2 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 3284 4554.5 1.38688
    53 no value ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]
    54 STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] 13884.4 19014.6 1.36949
    55 ZNF547 sedlin. [swissprot;acc:o14582] 22440 16388 1.36929
    56 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
    57 CDC37 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 8152.55 11134.8 1.36581
    58 DDX43 dead-box protein. [refseq;acc:nm_018665] 10628.3 14486 1.36296
    59 GLUD2 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 15863.6 11662.3 1.36025
    60 GNPDA1 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 11761 15924 1.35397
    61 CRISP2 testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 15352 11346.5 1.35302
    62 GLRA3 glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] 9418.7 12695.6 1.34791
    63 STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 8519.83 11453 1.34428
    64 LYZL1 similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 15264 20387 1.33563
    65 EP400 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 7853.67 10406.3 1.32502
    66 HS6ST2 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 11461 15180 1.32449
    67 no value presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 10793.5 14291.5 1.32408
    68 purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 8932.56 11823.3 1.32362
    69 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 7704.7 10174.1 1.32051
    70 protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 13975.7 10593.2 1.31931
    71 NUP43 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 4338.65 5700.79 1.31395
    72 PGAM4 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 4119 5397 1.31027
    73 no value phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]
    74 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 6742.5 8759.5 1.29915
    75 nanos (fragment). [sptrembl;acc:q8wy41] 8782 11350 1.29242
    76 spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 3474 2695 1.28905
    77 RCC1 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 8821.32 11366.5 1.28853
    78 no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 7584.72 9706.12 1.27969
    79 NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 9465.55 12106.5 1.27901
    80 DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 9102.34 11617.9 1.27636
    81 SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 14463 11356 1.2736
    82 no value dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 7706.5 6058 1.27212
    83 SNRPB small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] 18359.8 14447.8 1.27077
    84 STX1A syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] 12460.6 15781 1.26647
    85 TBL2 transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] 9688.47 12104.2 1.24934
    86 no value high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] 5677.96 4546.87 1.24876
    87 HMG1L1 dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] 5677.89 4547.43 1.24859
    88 HMG1L10 high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 5677.86 4547.66 1.24852
    89 SP100 nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] 5677.58 4549.85 1.24786
    90 HMG4L high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] 5677.45 4550.87 1.24755
    91 BMP8A bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 13841.2 11127.5 1.24387
    92 no value dok-like protein. [refseq;acc:nm_024872] 17571 21783 1.23971
    93 PMS2 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 7739.47 9580.95 1.23793
    94 TKTL1 transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 12946.3 10519.7 1.23067
    95 DUS1L pp3111 protein. [refseq;acc:nm_022156] 6185 7603 1.22926
    96 IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 8335.82 10228.3 1.22703
    97 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
    98 NR2E1 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] 7234.6 8858.94 1.22452
    99 ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 12787.8 10454.7 1.22316
    100 no value creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 9183.49 11217.7 1.22151

    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/