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 network_comparison green
    Results: HTML CSV LaTeX Showing element 2708 to 2757 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    170 BCL6 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Squared Subtracted High confidence 69165 16173.3 52991.7
    CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Divided 96730.5 1.39609 69286.7
    FES proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Ranked Low confidence 216.783 1.05714 205.066
    INADL inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799] Squared 67882.7 1.11441 60913.7
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured High confidence 23693.7 1.29736 18263
    PPP1R12A protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Subtracted Low confidence 8973.23 624.71 9597.94
    PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Squared 54860.1 5516 49344.1
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted High confidence 55.6161 11.1171 66.7332
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked 227.971 27.554 200.417
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Rooted Divided Low confidence 70.7428 1.06479 75.3259
    STRN striatin. [swissprot;acc:o43815] Subtracted 66.4354 4.5516 70.987
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Ranked Divided High confidence 227.199 1.17894 192.715
    VPS41 vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] Subtracted Low confidence 202.698 11.305 191.393
    171 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Rooted 98.0366 4.5502 93.4864
    CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared Divided High confidence 96602.7 1.39577 69211.2
    DAD1 defender against cell death 1 (dad-1). [swissprot;acc:p46966] Ranked Subtracted Low confidence 197.99 11.077 186.913
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided 219.889 1.05683 208.064
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Rooted High confidence 61.6639 1.16333 71.7355
    MAGED2 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] Measured 23693.7 1.29736 18263
    MPDZ multiple pdz domain protein. [refseq;acc:nm_003829] Squared Low confidence 67876.4 1.11438 60909.3
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Measured Subtracted High confidence 4117.67 1683.37 5801.04
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted Divided Low confidence 96.9641 1.06474 103.242
    RNF20 ring finger protein 20. [refseq;acc:nm_019592] Squared Subtracted 53551.4 5506.3 48045.1
    SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Measured Divided 7012.61 1.08158 7584.69
    SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Squared Subtracted High confidence 69165 16173.3 52991.7
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 11.1171 66.7332
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Ranked Divided 227.202 1.17829 192.823
    TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Measured Subtracted Low confidence 8749.42 622.91 9372.33
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Ranked High confidence 201.478 27.306 228.784
    172 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Rooted 55.6161 11.1171 66.7332
    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] Measured 4556.78 1611.52 2945.26
    ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Low confidence 10547.4 622.84 9924.56
    CAPZA1 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Ranked Divided 213.671 1.0567 202.205
    CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared High confidence 121579 1.39331 87259.3
    CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Subtracted 69123.3 16156.3 52967
    NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Measured Divided Low confidence 7012.61 1.08158 7584.69
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Ranked Subtracted 196.714 10.956 185.758
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Rooted Divided High confidence 56.7592 1.16261 65.9889
    SNRPA u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Subtracted Low confidence 70.5964 4.5235 75.1199
    SRM spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Squared 54936 5461.3 49474.7
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Ranked High confidence 201.515 27.237 228.752
    TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Divided 174.667 1.17685 205.556
    TRO trophinin. [swissprot;acc:q12816] Measured 23693.7 1.29736 18263
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Rooted Low confidence 65.0717 1.06436 69.26
    WBP11 ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Squared 67872.2 1.11437 60906.5
    173 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Ranked Subtracted 211.679 10.944 222.623
    methyltransferase like 2. [refseq;acc:nm_018396] Squared High confidence 71576.8 15250.1 56326.7
    ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Low confidence 43800.4 5442.1 38358.3
    BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Measured Divided High confidence 4579.34 1.29727 5940.64
    ELAC2 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Squared Low confidence 67872.2 1.11437 60906.5

    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/