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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2408 to 2457 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    301 SLC7A8 large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Ranked Low confidence 205.154 196.72 1.04287
    302 GTF2H3 tfiih basal transcription factor complex p34 subunit (basic transcription factor 2 34 kda subunit) (btf2-p34) (general transcription factor iih polypeptide 3). [swissprot;acc:q13889] Measured 9243.98 9781.77 1.05818
    HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared High confidence 28896.2 36767 1.27238
    ITGAV integrin alpha-v precursor (vitronectin receptor alpha subunit) (cd51 antigen). [swissprot;acc:p06756] Low confidence 57397.4 53011.1 1.08274
    PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured High confidence 5894.75 7073.65 1.19999
    PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted 203.673 182.638 1.11517
    RPL26 60s ribosomal protein l26. [swissprot;acc:q02877] Ranked 242.326 267.008 1.10185
    SMOC2 secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Rooted Low confidence 70.2592 74.0161 1.05347
    XPR1 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Ranked 209.12 200.548 1.04274
    303 CHDH choline dehydrogenase. [refseq;acc:nm_018397] Rooted 70.2592 74.0161 1.05347
    CRKL crk-like protein. [swissprot;acc:p46109] Squared High confidence 28896.2 36767 1.27238
    HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked Low confidence 210.057 201.45 1.04273
    ITGA8 integrin alpha-8. [swissprot;acc:p53708] Squared 57397.4 53011.1 1.08274
    NKX6-1 homeobox protein nkx-6.1. [swissprot;acc:p78426] Measured 9810.95 10381.3 1.05813
    PPP1CC serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] High confidence 22268.8 18560.4 1.1998
    PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 203.673 182.638 1.11517
    RPL35 60s ribosomal protein l35. [swissprot;acc:p42766] Ranked 242.333 266.999 1.10179
    304 no value 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 242.339 266.986 1.1017
    ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared 28896.2 36767 1.27238
    GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Rooted Low confidence 70.0111 73.7488 1.05339
    ITGA2B integrin alpha-iib precursor (platelet membrane glycoprotein iib) (gpalpha iib) (gpiib) (cd41 antigen). [swissprot;acc:p08514] Squared 57397.4 53011.1 1.08274
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked 209.232 200.662 1.04271
    NKX6-2 nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400] Measured 9810.95 10381.3 1.05813
    PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] High confidence 4855.46 5824.52 1.19958
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Rooted 203.673 182.638 1.11517
    305 FBLN2 fibulin-2 precursor. [swissprot;acc:p98095] Squared Low confidence 51256 47341.1 1.0827
    FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] High confidence 28896.2 36767 1.27238
    HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked Low confidence 210.05 201.454 1.04267
    LAPTM4B lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] Rooted 70.0674 73.7951 1.0532
    MRPL2 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Ranked High confidence 242.339 266.986 1.1017
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Measured 3856.29 4624.15 1.19912
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Rooted 203.673 182.638 1.11517
    TMED2 cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363] Measured Low confidence 9810.95 10381.3 1.05813
    306 no value 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked High confidence 242.153 266.673 1.10126
    pnas-18. [sptrembl;acc:q9bzu3] Measured 13680.5 11409.6 1.19903
    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] Squared Low confidence 49462.2 45684.1 1.0827
    FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] High confidence 28896.2 36767 1.27238
    HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Measured Low confidence 7941.76 8403.21 1.0581
    RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Rooted High confidence 56.3935 62.8817 1.11505
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Ranked Low confidence 202.122 193.867 1.04258
    TMEM115 pl6 protein (placental protein 6). [swissprot;acc:q12893] Rooted 70.0696 73.7968 1.05319
    307 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] Squared 49457.6 45681.4 1.08266
    CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Measured High confidence 12365.2 14824.9 1.19892
    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] Squared 28896.4 36766.8 1.27237
    HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Measured Low confidence 7943.99 8405.13 1.05805
    LAPTM4A lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] Rooted 70.0696 73.7968 1.05319
    PHKG1 phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (ec 2.7.1.38) (phosphorylase kinase gamma subunit 1). [swissprot;acc:q16816] Ranked 217.957 227.209 1.04245
    SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Rooted High confidence 50.4687 45.2733 1.11476
    SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Ranked 242.153 266.673 1.10126
    308 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] Squared 30596.2 38919.9 1.27205

    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/