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 Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2714 to 2763 of 66312 in total
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    170 Subtracted BCL6 Squared b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] High confidence 69165 16173.3 52991.7
    PPP1R12A Measured protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Low confidence 8973.23 624.71 9597.94
    PRKAG2 Squared 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 54860.1 5516 49344.1
    PRMT8 Rooted protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] High confidence 55.6161 11.1171 66.7332
    PRPF40B Ranked huntingtin interacting protein c. [refseq;acc:nm_012272] 227.971 27.554 200.417
    STRN Rooted striatin. [swissprot;acc:o43815] Low confidence 66.4354 4.5516 70.987
    VPS41 Ranked vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] 202.698 11.305 191.393
    171 Divided CTPS Squared ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] High confidence 96602.7 1.39577 69211.2
    FOXP3 Ranked forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Low confidence 219.889 1.05683 208.064
    LASS2 Rooted lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] High confidence 61.6639 1.16333 71.7355
    MAGED2 Measured 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] 23693.7 1.29736 18263
    MPDZ Squared multiple pdz domain protein. [refseq;acc:nm_003829] Low confidence 67876.4 1.11438 60909.3
    NFU1 Rooted hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 96.9641 1.06474 103.242
    SENP8 Measured sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] 7012.61 1.08158 7584.69
    TIAL1 Ranked nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] High confidence 227.202 1.17829 192.823
    Subtracted ATG4B Rooted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Low confidence 98.0366 4.5502 93.4864
    DAD1 Ranked defender against cell death 1 (dad-1). [swissprot;acc:p46966] 197.99 11.077 186.913
    NCBP2L Measured dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] High confidence 4117.67 1683.37 5801.04
    RNF20 Squared ring finger protein 20. [refseq;acc:nm_019592] Low confidence 53551.4 5506.3 48045.1
    SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] High confidence 69165 16173.3 52991.7
    SNRP70 Rooted u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 55.6161 11.1171 66.7332
    TRAPPC3 Measured bet3 homolog. [swissprot;acc:o43617] Low confidence 8749.42 622.91 9372.33
    TRPC4 Ranked short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] High confidence 201.478 27.306 228.784
    172 Divided CAPZA1 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Low confidence 213.671 1.0567 202.205
    CSTF2T Squared likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] High confidence 121579 1.39331 87259.3
    NEDD8 Measured ubiquitin-like protein nedd8. [swissprot;acc:q15843] Low confidence 7012.61 1.08158 7584.69
    SF3B1 Rooted splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] High confidence 56.7592 1.16261 65.9889
    TIPRL Ranked cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 174.667 1.17685 205.556
    TRO Measured trophinin. [swissprot;acc:q12816] 23693.7 1.29736 18263
    UNC84A Rooted sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Low confidence 65.0717 1.06436 69.26
    WBP11 Squared ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] 67872.2 1.11437 60906.5
    Subtracted no value Measured 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] High confidence 4556.78 1611.52 2945.26
    Rooted filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 55.6161 11.1171 66.7332
    ATG3 Measured apg3p; pc3-96 protein. [refseq;acc:nm_022488] Low confidence 10547.4 622.84 9924.56
    CTBP1 Squared c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] High confidence 69123.3 16156.3 52967
    PPM1B Ranked protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Low confidence 196.714 10.956 185.758
    SNRPA Rooted u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] 70.5964 4.5235 75.1199
    SRM Squared spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] 54936 5461.3 49474.7
    TBC1D10A Ranked ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] High confidence 201.515 27.237 228.752
    173 Divided BCAR3 Measured breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 4579.34 1.29727 5940.64
    ELAC2 Squared elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Low confidence 67872.2 1.11437 60906.5
    MRPS17 Rooted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] High confidence 145.551 1.1597 168.796
    SEPT2 Measured septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Low confidence 10168.5 1.08145 10996.7
    SEPT4 Squared septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] High confidence 82624.3 1.39258 115061
    SNRPA Rooted u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Low confidence 70.5964 1.06408 75.1199
    SNRPD1 Ranked small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] High confidence 227.032 1.17599 193.056
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Low confidence 221.678 1.05664 209.795
    Subtracted no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 211.679 10.944 222.623
    Squared methyltransferase like 2. [refseq;acc:nm_018396] 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

    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/