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 2425 to 2474 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] no value 242.339 Ranked High confidence 266.986 1.1017
    cytohesin 4. [swissprot;acc:q9uia0] PSCD4 203.673 Rooted 182.638 1.11517
    integrin alpha-iib precursor (platelet membrane glycoprotein iib) (gpalpha iib) (gpiib) (cd41 antigen). [swissprot;acc:p08514] ITGA2B 57397.4 Squared Low confidence 53011.1 1.08274
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] KHDRBS1 209.232 Ranked 200.662 1.04271
    nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400] NKX6-2 9810.95 Measured 10381.3 1.05813
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] PRPF31 4855.46 High confidence 5824.52 1.19958
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 28896.2 Squared 36767 1.27238
    rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] GIPC1 70.0111 Rooted Low confidence 73.7488 1.05339
    305 cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363] TMED2 9810.95 Measured 10381.3 1.05813
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 203.673 Rooted High confidence 182.638 1.11517
    fibulin-2 precursor. [swissprot;acc:p98095] FBLN2 51256 Squared Low confidence 47341.1 1.0827
    homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 210.05 Ranked 201.454 1.04267
    lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] LAPTM4B 70.0674 Rooted 73.7951 1.0532
    mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] MRPL2 242.339 Ranked High confidence 266.986 1.1017
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] OSR1 3856.29 Measured 4624.15 1.19912
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN 28896.2 Squared 36767 1.27238
    306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] no value 242.153 Ranked 266.673 1.10126
    pl6 protein (placental protein 6). [swissprot;acc:q12893] TMEM115 70.0696 Rooted Low confidence 73.7968 1.05319
    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] ATP2B1 49462.2 Squared 45684.1 1.0827
    pnas-18. [sptrembl;acc:q9bzu3] no value 13680.5 Measured High confidence 11409.6 1.19903
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] FGR 28896.2 Squared 36767 1.27238
    rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] RBM39 56.3935 Rooted 62.8817 1.11505
    serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] HTRA1 7941.76 Measured Low confidence 8403.21 1.0581
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF 202.122 Ranked 193.867 1.04258
    307 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] GRAP2 28896.4 Squared High confidence 36766.8 1.27237
    lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] LAPTM4A 70.0696 Rooted Low confidence 73.7968 1.05319
    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 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

    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/