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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 325 to 374 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    82 ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted 60.8022 79.5099 1.30768
    CCNG1 cyclin g1 (cyclin g). [swissprot;acc:p51959] Squared 117718 70505.8 1.66962
    GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Ranked 267.636 335.359 1.25304
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Measured 4172.91 5954.48 1.42694
    83 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 4932.27 7033.29 1.42597
    MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Ranked 88.2482 110.265 1.24949
    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] Rooted 63.6507 48.7127 1.30666
    PPP2R5A serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Squared 117718 70505.9 1.66962
    84 no value jun dimerization protein. [refseq;acc:nm_130469] Measured 4932.27 7033.29 1.42597
    BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Squared 117515 70412.3 1.66896
    MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Ranked 88.2482 110.265 1.24949
    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] Rooted 46.7419 60.9337 1.30362
    85 no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Ranked 88.2482 110.265 1.24949
    ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Squared 67438.6 40697 1.65709
    FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Measured 4941.95 7037.11 1.42395
    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] Rooted 46.7419 60.9337 1.30362
    86 FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Measured 4942.49 7037.32 1.42384
    KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Squared 105500 64146.3 1.64468
    MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Ranked 88.2482 110.265 1.24949
    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] Rooted 63.6205 48.8838 1.30146
    87 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 42.2825 54.9687 1.30003
    FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Measured 4944.3 7038.04 1.42347
    MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Ranked 88.2482 110.265 1.24949
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Squared 105482 64136.9 1.64464
    88 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Ranked 88.2482 110.265 1.24949
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Squared 105482 64137.2 1.64463
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Measured 2411.93 1695.45 1.42259
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted 37.3005 48.4141 1.29795
    89 CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Measured 2414.22 1698.12 1.4217
    HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Squared 105473 64132.3 1.64462
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked 88.2482 110.265 1.24949
    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 1.29795
    90 no value transforming protein n-ras. [swissprot;acc:p01111] Squared 105469 64130.2 1.64461
    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] Rooted 37.3005 48.4141 1.29795
    KCND3 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Measured 2414.77 1698.75 1.4215
    NDN necdin. [swissprot;acc:q99608] Ranked 88.2482 110.265 1.24949
    91 CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted 37.3005 48.4141 1.29795
    KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Measured 2416.53 1700.8 1.42082
    MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Ranked 88.2482 110.265 1.24949
    RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared 90432.9 56304.2 1.60615
    92 MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked 88.2482 110.265 1.24949
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Measured 4117.67 5801.04 1.40882
    PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Squared 29570.7 18601.8 1.58967
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Rooted 37.3005 48.4141 1.29795
    93 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Measured 4245.52 5942.75 1.39977
    ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Squared 29567 18601.6 1.58949
    CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Rooted 37.3005 48.4141 1.29795
    MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Ranked 88.2482 110.265 1.24949
    94 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured 4247.86 5941.88 1.39879
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Ranked 88.2482 110.265 1.24949

    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/