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 Value Type description 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
    		Value Type
    		description
    		red
    		green
    		network_comparison
    82 ATF3 Rooted cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 60.8022 79.5099 1.30768
    CCNG1 Squared cyclin g1 (cyclin g). [swissprot;acc:p51959] 117718 70505.8 1.66962
    GNB5 Ranked guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] 267.636 335.359 1.25304
    SNRPD1 Measured small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 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 Ranked melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 88.2482 110.265 1.24949
    PPP2R1B Rooted 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] 63.6507 48.7127 1.30666
    PPP2R5A Squared 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] 117718 70505.9 1.66962
    84 no value Measured jun dimerization protein. [refseq;acc:nm_130469] 4932.27 7033.29 1.42597
    BRAF Squared b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 117515 70412.3 1.66896
    MAGEE2 Ranked hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 88.2482 110.265 1.24949
    NFYC Rooted 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] 46.7419 60.9337 1.30362
    85 no value Ranked melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 88.2482 110.265 1.24949
    ATG12 Squared autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 67438.6 40697 1.65709
    FOSL2 Measured fos-related antigen 2. [swissprot;acc:p15408] 4941.95 7037.11 1.42395
    NFYA Rooted 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] 46.7419 60.9337 1.30362
    86 FOSB Measured protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 4942.49 7037.32 1.42384
    KRAS Squared transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 105500 64146.3 1.64468
    MAGEA11 Ranked melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 88.2482 110.265 1.24949
    PPP2R1A Rooted 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] 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 Measured fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 4944.3 7038.04 1.42347
    MAGEA2B Ranked melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 88.2482 110.265 1.24949
    SHOC2 Squared leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 105482 64136.9 1.64464
    88 no value Ranked hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 88.2482 110.265 1.24949
    Squared ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 105482 64137.2 1.64463
    KCND2 Measured potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 2411.93 1695.45 1.42259
    PSEN2 Rooted presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 37.3005 48.4141 1.29795
    89 CTH Measured cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 2414.22 1698.12 1.4217
    HRAS Squared transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 105473 64132.3 1.64462
    MAGEA6 Ranked melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 88.2482 110.265 1.24949
    SKP1A Rooted 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] 37.3005 48.4141 1.29795
    90 no value Squared transforming protein n-ras. [swissprot;acc:p01111] 105469 64130.2 1.64461
    FBXW7 Rooted 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 1.29795
    KCND3 Measured 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] 2414.77 1698.75 1.4215
    NDN Ranked necdin. [swissprot;acc:q99608] 88.2482 110.265 1.24949
    91 CUL2 Rooted cullin homolog 2 (cul-2). [swissprot;acc:q13617] 37.3005 48.4141 1.29795
    KCND1 Measured potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 2416.53 1700.8 1.42082
    MAGED1 Ranked melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 88.2482 110.265 1.24949
    RALGDS Squared ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 90432.9 56304.2 1.60615
    92 MAGEF1 Ranked melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 88.2482 110.265 1.24949
    NCBP2L Measured dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 4117.67 5801.04 1.40882
    PITRM1 Squared metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 29570.7 18601.8 1.58967
    PSEN1 Rooted presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 37.3005 48.4141 1.29795
    93 no value Measured formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 4245.52 5942.75 1.39977
    ALG1 Squared beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 29567 18601.6 1.58949
    CUL1 Rooted cullin homolog 1 (cul-1). [swissprot;acc:q13616] 37.3005 48.4141 1.29795
    MAGEB6B Ranked melanoma antigen, family b, 6. [refseq;acc:nm_173523] 88.2482 110.265 1.24949
    94 no value Measured huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 4247.86 5941.88 1.39879
    Ranked melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 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/