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 Value Type Hugo description Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 2430 to 2479 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    304 Squared ITGA2B integrin alpha-iib precursor (platelet membrane glycoprotein iib) (gpalpha iib) (gpiib) (cd41 antigen). [swissprot;acc:p08514] Low confidence 1.08274 57397.4 53011.1
    Rooted GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 1.05339 70.0111 73.7488
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] High confidence 1.11517 203.673 182.638
    305 Measured OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 1.19912 3856.29 4624.15
    TMED2 cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363] Low confidence 1.05813 9810.95 10381.3
    Ranked HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 1.04267 210.05 201.454
    MRPL2 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] High confidence 1.1017 242.339 266.986
    Squared FBLN2 fibulin-2 precursor. [swissprot;acc:p98095] Low confidence 1.0827 51256 47341.1
    FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] High confidence 1.27238 28896.2 36767
    Rooted LAPTM4B lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] Low confidence 1.0532 70.0674 73.7951
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] High confidence 1.11517 203.673 182.638
    306 Measured no value pnas-18. [sptrembl;acc:q9bzu3] 1.19903 13680.5 11409.6
    HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Low confidence 1.0581 7941.76 8403.21
    Ranked no value 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] High confidence 1.10126 242.153 266.673
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Low confidence 1.04258 202.122 193.867
    Squared ATP2B1 plasma membrane calcium-transporting atpase 1 (ec 3.6.3.8) (pmca1) (plasma membrane calcium pump isoform 1) (plasma membrane calcium atpase isoform 1). [swissprot;acc:p20020] 1.0827 49462.2 45684.1
    FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] High confidence 1.27238 28896.2 36767
    Rooted RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 1.11505 56.3935 62.8817
    TMEM115 pl6 protein (placental protein 6). [swissprot;acc:q12893] Low confidence 1.05319 70.0696 73.7968
    307 Measured CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] High confidence 1.19892 12365.2 14824.9
    HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Low confidence 1.05805 7943.99 8405.13
    Ranked PHKG1 phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (ec 2.7.1.38) (phosphorylase kinase gamma subunit 1). [swissprot;acc:q16816] 1.04245 217.957 227.209
    SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] High confidence 1.10126 242.153 266.673
    Squared ATP2B4 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] Low confidence 1.08266 49457.6 45681.4
    GRAP2 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] High confidence 1.27237 28896.4 36766.8
    Rooted LAPTM4A lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] Low confidence 1.05319 70.0696 73.7968
    SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] High confidence 1.11476 50.4687 45.2733
    308 Measured DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 1.19878 4977.09 5966.44
    HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Low confidence 1.05804 7944.21 8405.32
    Ranked HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 1.0424 210.018 201.475
    RPL34 60s ribosomal protein l34. [swissprot;acc:p49207] High confidence 1.10126 242.153 266.673
    Squared AGPAT3 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] 1.27205 30596.2 38919.9
    GRPEL2 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Low confidence 1.08264 51507 47575.4
    Rooted DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] High confidence 1.11476 50.4687 45.2733
    SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Low confidence 1.05317 71.2747 75.0643
    309 Measured DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] High confidence 1.19855 4977.8 5966.14
    RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5] Low confidence 1.05803 10765.1 10174.7
    Ranked no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 1.04222 200.213 192.103
    SEC61A2 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] High confidence 1.10126 242.153 266.673
    Squared ATP2B2 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] Low confidence 1.0825 49436.8 45669.2
    CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] High confidence 1.27203 28900.8 36762.6
    Rooted no value u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 1.11424 56.185 62.6036
    SOAT2 sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] Low confidence 1.05316 69.5565 73.2539
    310 Measured HTRA2 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] 1.05802 7945.12 8406.1
    SART1 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] High confidence 1.19736 4909.79 5878.79
    Ranked NDUFA9 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] Low confidence 1.04186 205.75 197.484
    SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] High confidence 1.10126 242.153 266.673
    Squared CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 1.27198 28901.4 36762.1
    UBE2I 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] Low confidence 1.08239 59360.2 64250.6
    Rooted no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] High confidence 1.11406 95.0526 85.3206

    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/