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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 51 to 100 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    26 CYP27A1 cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] Low confidence 286.347 238.454 1.20085
    PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] High confidence 58 44 1.31818
    27 CYP24A1 cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] Low confidence 284.798 237.743 1.19792
    SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] High confidence 58 44 1.31818
    28 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Low confidence 142 170 1.19718
    ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence 201.949 153.671 1.31416
    29 Low confidence 203.115 170.557 1.19089
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] High confidence 187.458 243.678 1.29991
    30 no value serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 187.457
    BOK bcl2-related ovarian killer. [refseq;acc:nm_032515] Low confidence 265.638 223.235 1.18995
    31 DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 57.395 48.8186 1.17568
    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] High confidence 187.458 243.677 1.2999
    32 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] 187.462 243.673 1.29985
    PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Low confidence 273.188 232.49 1.17505
    33 MAP2K4 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] 210.241 246.125 1.17068
    PPP2R1B serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] High confidence 188.688 242.742 1.28647
    34 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] 189.07 242.453 1.28235
    UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Low confidence 155.56 133.876 1.16197
    35 NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] High confidence 260.532 204.309 1.27519
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Low confidence 297.273 258.59 1.14959
    36 NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] High confidence 260.532 204.309 1.27519
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Low confidence 296.837 258.33 1.14906
    37 CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 250.244 217.843 1.14874
    PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] High confidence 322 253 1.27273
    38 GNPDA2 glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] Low confidence 247.202 282.937 1.14456
    MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] High confidence 322 253 1.27273
    39 GNPDA1 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Low confidence 247.202 282.937 1.14456
    PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] High confidence 322 253 1.27273
    40 FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
    SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Low confidence 255.382 223.538 1.14245
    41 no value protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] High confidence 322 253 1.27273
    GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Low confidence 228.147 200.55 1.13761
    42 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] High confidence 204.641 160.957 1.2714
    GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Low confidence 227.371 200.532 1.13384
    43 no value jun dimerization protein. [refseq;acc:nm_130469] High confidence 204.641 160.957 1.2714
    RGS12 regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Low confidence 247.768 219.841 1.12703
    44 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] High confidence 204.641 161.046 1.2707
    PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Low confidence 242.742 217.217 1.11751
    45 FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence 204.641 161.051 1.27066
    MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Low confidence 242.742 217.217 1.11751
    46 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] High confidence 204.642 161.068 1.27053
    PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Low confidence 242.742 217.217 1.11751
    47 FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
    TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] High confidence 325.586 256.492 1.26938
    48 no value protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Low confidence 242.742 217.217 1.11751
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence 65.4586 83.0461 1.26868
    49 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 133 105 1.26667
    TBX19 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Low confidence 225.438 202.569 1.11289
    50 ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] High confidence 133 105 1.26667
    JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Low confidence 234.802 260.98 1.11149

    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/