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 Network Comparison Type Gene Hugo description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1380 to 1429 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    173 Divided SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked 227.032 193.056 1.17599
    Subtracted no value methyltransferase like 2. [refseq;acc:nm_018396] Squared 71576.8 56326.7 15250.1
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Measured 4556.79 2945.28 1611.51
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted 37.3005 48.4141 11.1136
    TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Ranked 201.515 228.752 27.237
    174 Divided DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 335 286 1.17133
    MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Measured 4455.95 5774.03 1.2958
    PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Rooted 145.551 168.796 1.1597
    ZNF547 sedlin. [swissprot;acc:o14582] Squared 112820 157033 1.39189
    Subtracted DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 71576.8 56326.7 15250.1
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Ranked 228.1 200.968 27.132
    PPP2R2B serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Measured 4556.83 2945.38 1611.45
    SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Rooted 37.3005 48.4141 11.1136
    175 Divided no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Squared 112820 157033 1.39189
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked 199.949 234.187 1.17123
    MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Measured 4456.67 5773.77 1.29553
    PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Rooted 145.551 168.796 1.1597
    Subtracted FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 37.3005 48.4141 11.1136
    FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared 71576.8 56326.7 15250.1
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Ranked 228.085 201.006 27.079
    PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Measured 4556.99 2945.8 1611.19
    176 Divided MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 4456.93 5773.67 1.29544
    PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Rooted 145.551 168.796 1.1597
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Ranked 275.754 235.908 1.1689
    TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Squared 112820 157033 1.39189
    Subtracted CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted 37.3005 48.4141 11.1136
    EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked 271.016 244.167 26.849
    HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Measured 10235.2 11830.8 1595.6
    PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Squared 71576.8 56326.7 15250.1
    177 Divided NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked 229.406 196.695 1.1663
    RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Measured 4457.06 5773.63 1.29539
    SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Squared 78383 108483 1.38401
    SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Rooted 145.551 168.796 1.1597
    Subtracted ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Squared 9924.76 25146.6 15221.8
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured 4110.14 5694.99 1584.85
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Rooted 37.3005 48.4141 11.1136
    SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked 241.07 267.88 26.81
    178 Divided no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 226.887 194.72 1.1652
    CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] Squared 25326.4 18354.1 1.37988
    MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Measured 21591.5 27904.5 1.29238
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Rooted 45.7414 52.932 1.1572
    Subtracted ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Squared 9924.76 25146.6 15221.8
    CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Measured 10908.6 12491.8 1583.2
    CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Rooted 37.3005 48.4141 11.1136
    DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Ranked 241.07 267.88 26.81
    179 Divided no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 226.884 194.79 1.16476
    CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Squared 25326.3 18354.1 1.37987
    EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Rooted 50.272 43.4634 1.15665
    MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Measured 21591.5 27904.5 1.29238
    Subtracted NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 4266.04 5843.51 1577.47

    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/