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 [...,...].
    Gene Rank description Hugo Network Comparison Type red Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2451 to 2500 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    307 phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (ec 2.7.1.38) (phosphorylase kinase gamma subunit 1). [swissprot;acc:q16816] PHKG1 217.957 Ranked Low confidence 227.209 1.04245
    plasma membrane calcium-transporting atpase 4 (ec 3.6.3.8) (pmca4) (plasma membrane calcium pump isoform 4) (plasma membrane calcium atpase isoform 4). [swissprot;acc:p23634] ATP2B4 49457.6 Squared 45681.4 1.08266
    probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] HTRA3 7943.99 Measured 8405.13 1.05805
    serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR 242.153 Ranked High confidence 266.673 1.10126
    t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] CCT3 12365.2 Measured 14824.9 1.19892
    transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] SIN3A 50.4687 Rooted 45.2733 1.11476
    308 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] AGPAT3 30596.2 Squared 38919.9 1.27205
    60s ribosomal protein l34. [swissprot;acc:p49207] RPL34 242.153 Ranked 266.673 1.10126
    density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] DENR 50.4687 Rooted 45.2733 1.11476
    grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] GRPEL2 51507 Squared Low confidence 47575.4 1.08264
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 210.018 Ranked 201.475 1.0424
    probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] HTRA4 7944.21 Measured 8405.32 1.05804
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] DVL1 4977.09 High confidence 5966.44 1.19878
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 71.2747 Rooted Low confidence 75.0643 1.05317
    309 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 28900.8 Squared High confidence 36762.6 1.27203
    microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] no value 200.213 Ranked Low confidence 192.103 1.04222
    plasma membrane calcium-transporting atpase 2 (ec 3.6.3.8) (pmca2) (plasma membrane calcium pump isoform 2) (plasma membrane calcium atpase isoform 2). [swissprot;acc:q01814] ATP2B2 49436.8 Squared 45669.2 1.0825
    protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2 242.153 Ranked High confidence 266.673 1.10126
    ras-related protein rab-26. [swissprot;acc:q9ulw5] RAB26 10765.1 Measured Low confidence 10174.7 1.05803
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] DVL2 4977.8 High confidence 5966.14 1.19855
    sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] SOAT2 69.5565 Rooted Low confidence 73.2539 1.05316
    u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] no value 56.185 High confidence 62.6036 1.11424
    310 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 28901.4 Squared 36762.1 1.27198
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value 95.0526 Rooted 85.3206 1.11406
    nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795] NDUFA9 205.75 Ranked Low confidence 197.484 1.04186
    protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] SEC61A1 242.153 High confidence 266.673 1.10126
    serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] HTRA1 72.0177 Rooted Low confidence 75.8419 1.0531
    serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] HTRA2 7945.12 Measured 8406.1 1.05802
    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] SART1 4909.79 High confidence 5878.79 1.19736
    ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] UBE2I 59360.2 Squared Low confidence 64250.6 1.08239
    311 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] AGPAT4 30566.4 High confidence 38866.5 1.27154
    myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4 95.0526 Rooted 85.3206 1.11406
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 7398.26 Measured Low confidence 7826.48 1.05788
    protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] EIF1B 242.627 Ranked High confidence 267.151 1.10108
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 4981.52 Measured 5964.58 1.19734
    sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610] SOAT1 69.568 Rooted Low confidence 73.2622 1.0531
    ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] UBE1C 192.088 Ranked 184.374 1.04184
    wd-repeat protein an11 homolog. [swissprot;acc:o15491] WDR68 49674.5 Squared 45895.5 1.08234
    312 60s ribosomal protein l3-like. [swissprot;acc:q92901] RPL3L 242.195 Ranked High confidence 266.663 1.10103
    coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] BICD2 7696.96 Measured Low confidence 8141.6 1.05777
    ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] FTSJ3 50189.4 Squared 46383.9 1.08204
    methyltransferase like 2. [refseq;acc:nm_018396] no value 71576.8 High confidence 56326.7 1.27074
    myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] MYH8 95.0526 Rooted 85.3206 1.11406
    ring finger protein 10. [refseq;acc:nm_014868] RNF10 69.5675 Low confidence 73.2618 1.0531
    u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] SNRPA1 202.051 Ranked 193.937 1.04184
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] no value 4598.21 Measured High confidence 5500.48 1.19622
    313 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 202.05 Ranked Low confidence 193.94 1.04182
    bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] BICD1 7696.96 Measured 8141.6 1.05777
    cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] DYNLT1 71576.8 Squared High confidence 56326.7 1.27074
    endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] no value 51313.9 Low confidence 47442 1.08161

    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/