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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 473 to 522 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 Measured Divided 4489.19 2765.82 1.6231
    cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] CTH Ranked Subtracted 269.254 327.655 58.401
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] GNG8 Divided 266.864 336.184 1.25976
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] MAGEA6 Squared 219048 129762 1.68808
    melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 Rooted Subtracted 137.446 120.823 16.623
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] PPP1R2 Squared 192904 126167 66737
    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] SON Rooted Divided 35.6294 49.8119 1.39806
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] no value Measured Subtracted 16771.5 12889.1 3882.4
    61 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 6475.5 10307.5 3832
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB Divided 4489.19 2765.82 1.6231
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] GNG5 Ranked 266.864 336.182 1.25975
    kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] KCNIP1 Rooted 43.4291 31.7159 1.36932
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 Subtracted 137.446 120.823 16.623
    necdin. [swissprot;acc:q99608] NDN Squared Divided 219048 129762 1.68808
    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] KCND3 Ranked Subtracted 269.248 327.642 58.394
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] PPP1R2P9 Squared 192779 126095 66684
    62 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 Measured 6475.5 10307.5 3832
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL Divided 4489.19 2765.82 1.6231
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] GNG10 Ranked 266.865 336.181 1.25974
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value Rooted Subtracted 137.446 120.823 16.623
    melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] MAGED1 Squared Divided 219048 129762 1.68808
    potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] KCNIP4 Rooted 43.4519 31.7522 1.36847
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] KCND1 Ranked Subtracted 269.23 327.601 58.371
    ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] RRS1 Squared 189976 124480 65496
    63 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] no value Ranked Divided 266.865 336.178 1.25973
    kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] KCNIP2 Rooted 43.4554 31.7576 1.36835
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Subtracted 137.446 120.823 16.623
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] MAGEF1 Squared Divided 219048 129762 1.68808
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] MYO15A Measured 4489.19 2765.82 1.6231
    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] NFYC Ranked Subtracted 260.532 204.309 56.223
    serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] PPP1CA Squared 189976 124480 65496
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Measured 6475.5 10307.5 3832
    64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 Rooted Divided 63.8686 47.2654 1.35128
    amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2 Measured Subtracted 6475.5 10307.5 3832
    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] NFYA Ranked 260.532 204.309 56.223
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A Squared 144940 81169.7 63770.3
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] PYGM Measured Divided 4489.19 2765.82 1.6231
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 Ranked 266.868 336.159 1.25965
    melanoma antigen, family b, 6. [refseq;acc:nm_173523] MAGEB6B Squared 219048 129762 1.68808
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Rooted Subtracted 137.446 120.823 16.623
    65 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] CSTF3 Measured 22515.5 18702.6 3812.9
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB Rooted Divided 63.8686 47.2654 1.35128
    guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] GNAQ Ranked 267.136 336.077 1.25807
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] no value Squared 219048 129762 1.68808
    melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 Rooted Subtracted 137.446 120.823 16.623
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B Squared 144912 81155 63757
    neuralized-like. [refseq;acc:nm_004210] NEURL Measured Divided 1657.68 2690.25 1.6229
    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] no value Ranked Subtracted 187.457 243.678 56.221
    66 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF Measured 17757.5 14008 3749.5
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL Rooted Divided 63.8686 47.2654 1.35128

    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/