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 Network Comparison Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 475 to 524 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		Network Comparison Type
    		description
    		red
    		green
    		network_comparison
    60 GBE1 Measured Divided 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 2765.82 1.6231
    GNG8 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 266.864 336.184 1.25976
    MAGEA6 Squared melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 219048 129762 1.68808
    MAGEC1 Rooted Subtracted melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 137.446 120.823 16.623
    PPP1R2 Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 192904 126167 66737
    SON Rooted Divided 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] 35.6294 49.8119 1.39806
    61 ARRB2 Measured Subtracted beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 6475.5 10307.5 3832
    GNG5 Ranked Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 266.864 336.182 1.25975
    KCND3 Subtracted 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] 269.248 327.642 58.394
    KCNIP1 Rooted Divided kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 43.4291 31.7159 1.36932
    MAGEA4 Subtracted melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 137.446 120.823 16.623
    NDN Squared Divided necdin. [swissprot;acc:q99608] 219048 129762 1.68808
    PPP1R2P9 Subtracted type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 192779 126095 66684
    PYGB Measured Divided glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 4489.19 2765.82 1.6231
    62 no value Rooted Subtracted melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 137.446 120.823 16.623
    ARRB1 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 10307.5 3832
    GNG10 Ranked Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 266.865 336.181 1.25974
    KCND1 Subtracted potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 269.23 327.601 58.371
    KCNIP4 Rooted Divided potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 43.4519 31.7522 1.36847
    MAGED1 Squared melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 219048 129762 1.68808
    PYGL Measured glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 4489.19 2765.82 1.6231
    RRS1 Squared Subtracted ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 189976 124480 65496
    63 no value Ranked Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 266.865 336.178 1.25973
    KCNIP2 Rooted 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] 43.4554 31.7576 1.36835
    MAGEA10 Subtracted melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 137.446 120.823 16.623
    MAGEF1 Squared Divided melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 219048 129762 1.68808
    MYO15A Measured myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 4489.19 2765.82 1.6231
    NFYC Ranked Subtracted 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] 260.532 204.309 56.223
    PPP1CA Squared serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 189976 124480 65496
    SPATA6 Measured spermatogenesis associated 6. [refseq;acc:nm_019073] 6475.5 10307.5 3832
    64 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
    ATG4A Squared cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 144940 81169.7 63770.3
    GBE1 Rooted Divided 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 63.8686 47.2654 1.35128
    GNG11 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 336.159 1.25965
    MAGEB4 Rooted Subtracted melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 137.446 120.823 16.623
    MAGEB6B Squared Divided melanoma antigen, family b, 6. [refseq;acc:nm_173523] 219048 129762 1.68808
    NFYA Ranked Subtracted 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] 260.532 204.309 56.223
    PYGM Measured Divided glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 4489.19 2765.82 1.6231
    65 no value Ranked Subtracted 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] 187.457 243.678 56.221
    Squared Divided melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 219048 129762 1.68808
    CSTF3 Measured Subtracted cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 22515.5 18702.6 3812.9
    GNAQ Ranked Divided guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 267.136 336.077 1.25807
    MAGED2 Rooted Subtracted 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] 137.446 120.823 16.623
    MAP1LC3B Squared microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 144912 81155 63757
    NEURL Measured Divided neuralized-like. [refseq;acc:nm_004210] 1657.68 2690.25 1.6229
    PYGB Rooted glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 63.8686 47.2654 1.35128
    66 ARAF Measured Subtracted a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 17757.5 14008 3749.5
    GNA11 Ranked Divided guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 267.136 336.077 1.25807
    MAGEA9 Squared melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 219048 129762 1.68808
    MAP1LC3A Subtracted microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 144911 81154.7 63756.3

    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/