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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 832 to 881 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    104 Rooted vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] VPS18 Low confidence 1.08594 69.2771 75.2308
    105 Measured musashi 1. [refseq;acc:nm_002442] MSI1 High confidence 1.36996 4241.57 5810.79
    ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Low confidence 1.09949 10585.5 11638.6
    Ranked guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] GNB1 High confidence 1.24914 266.716 333.165
    transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] E2F1 Low confidence 1.07369 220.497 205.364
    Squared cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 High confidence 1.54656 407289 263351
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] PPP1R2 Low confidence 1.16399 62385.1 53596
    Rooted fos-related antigen 2. [swissprot;acc:p15408] FOSL2 High confidence 1.27682 60.8675 77.7168
    vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] VPS33B Low confidence 1.08385 69.4249 75.2464
    106 Measured nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 High confidence 1.36996 4241.57 5810.79
    vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] VPS18 Low confidence 1.09789 7337.57 8055.84
    Ranked transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 1.07369 220.497 205.364
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] COQ7 High confidence 1.24913 252.329 202.004
    Squared atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] ATP5O Low confidence 1.1634 61860.4 53172.3
    cytohesin 4. [swissprot;acc:q9uia0] PSCD4 High confidence 1.54656 407289 263351
    Rooted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 Low confidence 1.0833 57.5193 53.0965
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB High confidence 1.27678 60.8692 77.7165
    107 Measured 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 1.36977 4266.04 5843.51
    tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] TP53I3 Low confidence 1.09746 11371 12479.2
    Ranked homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 High confidence 1.24907 252.309 201.998
    mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] FAM89B Low confidence 1.07293 227.429 211.97
    Squared cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 High confidence 1.54656 407289 263351
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] PPP1R2P9 Low confidence 1.16176 62040.9 53402.5
    Rooted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 High confidence 1.27664 60.875 77.7152
    junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 Low confidence 1.0833 57.5193 53.0965
    108 Measured filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] FLNB High confidence 1.35116 4366.44 5899.76
    septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] SEPT1 Low confidence 1.09685 10499 11515.8
    Ranked disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] DLGAP3 1.07251 197.731 212.069
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 High confidence 1.24902 252.296 201.995
    Squared glycogen debranching enzyme (glycogen debrancher) [includes: 4-alpha- glucanotransferase (ec 2.4.1.25) (oligo-1,4-1,4-glucantransferase); amylo-alpha-1,6-glucosidase (ec 3.2.1.33) (amylo-1,6-glucosidase) (dextrin 6-alpha-d-glucosidase)]. [swissprot;acc:p35573] AGL Low confidence 1.16086 61349.6 52848.4
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value High confidence 1.54043 19321 12542.6
    Rooted sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] SMPD2 Low confidence 1.0833 57.5193 53.0965
    voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] CACNG2 High confidence 1.26585 49.2925 62.397
    109 Measured rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 1.35116 4366.44 5899.76
    vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] VPS33B Low confidence 1.0966 7354.65 8065.08
    Ranked guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] GNB4 High confidence 1.24856 266.933 333.281
    neuralized-like. [refseq;acc:nm_004210] NEURL Low confidence 1.07239 232.704 216.996
    Squared atp synthase d chain, mitochondrial (ec 3.6.3.14) (my032 protein). [swissprot;acc:o75947] ATP5H 1.15666 59868.5 51759.6
    myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4 High confidence 1.54043 19321 12542.6
    Rooted db83 protein. [swissprot;acc:p57088] TMEM33 Low confidence 1.0833 57.5193 53.0965
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] CACNG8 High confidence 1.26585 49.2923 62.3969
    110 Measured high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] HMG20B Low confidence 1.09572 7206.99 7896.81
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 High confidence 1.35116 4366.44 5899.76
    Ranked deltex 2. [refseq;acc:nm_020892] DTX2 1.2459 333.144 267.393
    disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] no value Low confidence 1.07221 197.752 212.031
    Squared intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] 1.15306 60017 52050.3
    myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] MYH8 High confidence 1.54043 19321 12542.6
    Rooted high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] HMG20B Low confidence 1.08252 69.0515 74.7493
    voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] CACNG4 High confidence 1.26585 49.293 62.3973
    111 Measured melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] MAGED4 Low confidence 1.0937 11285.3 10318.5

    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/