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 Network Comparison Type Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2451 to 2500 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		red
    		green
    		network_comparison
    307 CCT3 Divided Measured t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 12365.2 14824.9 1.19892
    GRAP2 Squared grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] 28896.4 36766.8 1.27237
    MAGEA6 Subtracted Ranked melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 88.2482 110.265 22.0168
    SIN3A Divided Rooted transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 50.4687 45.2733 1.11476
    SRR Ranked serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] 242.153 266.673 1.10126
    WASL Subtracted Rooted neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 66.0989 74.0609 7.962
    308 ADC Squared ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] 32991.5 40704.5 7713
    AGPAT3 Divided 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 30596.2 38919.9 1.27205
    BHLHB4 Subtracted Measured ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 11852.9 10773.5 1079.4
    DENR Divided Rooted density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 50.4687 45.2733 1.11476
    DVL1 Measured segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 4977.09 5966.44 1.19878
    NDN Subtracted Ranked necdin. [swissprot;acc:q99608] 88.2482 110.265 22.0168
    RPL34 Divided 60s ribosomal protein l34. [swissprot;acc:p49207] 242.153 266.673 1.10126
    RPS6KC1 Subtracted Rooted ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 65.9938 73.9449 7.9511
    309 no value Divided u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 56.185 62.6036 1.11424
    Subtracted ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 65.9938 73.9449 7.9511
    AZIN1 Squared ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] 32987.4 40698.5 7711.1
    BHLHB5 Measured basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 11848.8 10770.3 1078.5
    CUTL1 Divided Squared ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 28900.8 36762.6 1.27203
    DVL2 Measured segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 4977.8 5966.14 1.19855
    MAGED1 Subtracted Ranked melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 88.2482 110.265 22.0168
    SEC61A2 Divided protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] 242.153 266.673 1.10126
    310 no value Rooted myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 95.0526 85.3206 1.11406
    Subtracted Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 7551.8 8630.06 1078.26
    C15orf15 Squared ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 30651.3 38253.3 7602
    CUTL2 Divided homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 28901.4 36762.1 1.27198
    MAGEF1 Subtracted Ranked melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 88.2482 110.265 22.0168
    SART1 Divided Measured squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] 4909.79 5878.79 1.19736
    SEC61A1 Ranked protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 242.153 266.673 1.10126
    TXNL4A Subtracted Rooted spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 56.9506 64.7888 7.8382
    311 no value Squared 40s ribosomal protein s28. [swissprot;acc:p25112] 30682.9 38183.6 7500.7
    AGPAT4 Divided 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 30566.4 38866.5 1.27154
    APBA1 Subtracted Measured amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 2820.51 3897.1 1076.59
    DVL3 Divided segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 4981.52 5964.58 1.19734
    EIF1B Ranked protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] 242.627 267.151 1.10108
    MAGEB6B Subtracted melanoma antigen, family b, 6. [refseq;acc:nm_173523] 88.2482 110.265 22.0168
    MYH4 Divided Rooted myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 95.0526 85.3206 1.11406
    RRM2B Subtracted ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 62.3337 70.0738 7.7401
    312 no value Divided Measured u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 4598.21 5500.48 1.19622
    Squared methyltransferase like 2. [refseq;acc:nm_018396] 71576.8 56326.7 1.27074
    Subtracted Ranked melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 88.2482 110.265 22.0168
    DNALI1 Squared axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 33044.3 40524.8 7480.5
    MAX Measured max protein. [swissprot;acc:p25912] 4640.26 5704.87 1064.61
    MYH8 Divided Rooted myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 95.0526 85.3206 1.11406
    NOSTRIN Subtracted nostrin. [refseq;acc:nm_052946] 59.6399 51.9242 7.7157
    RPL3L Divided Ranked 60s ribosomal protein l3-like. [swissprot;acc:q92901] 242.195 266.663 1.10103
    313 DYNLT1 Squared cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 71576.8 56326.7 1.27074
    FBLN2 Subtracted fibulin-2 precursor. [swissprot;acc:p98095] 45189.6 52666.2 7476.6
    LSM5 Measured u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 4567.04 5631.2 1064.16
    MAGEA9 Ranked melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 88.2482 110.265 22.0168

    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/