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 network_comparison green
    Results: HTML CSV LaTeX Showing element 1094 to 1143 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		network_comparison
    		green
    137 NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Measured Divided 3620.77 1.31556 4763.34
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked 350 1.2069 290
    SGTA small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Squared Subtracted 69549 23404.5 92953.5
    138 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Rooted 49.293 13.1043 62.3973
    HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared 70739 23169.8 93908.8
    KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Measured Divided 2755.15 1.31555 2094.3
    MSI1 musashi 1. [refseq;acc:nm_002442] Rooted 54.9787 1.20486 66.2416
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Ranked 194.372 1.20493 234.204
    TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Subtracted 174.667 30.889 205.556
    TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Measured 15182.5 1904.6 13277.9
    UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Squared Divided 468498 1.45156 322755
    139 APBA1 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] Ranked 271.752 1.20415 225.68
    CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Rooted Subtracted 49.3267 13.09 62.4167
    CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Squared Divided 81592.1 1.45153 56211.1
    CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Measured Subtracted 12780.7 1904.3 10876.4
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Ranked 287.41 30.575 256.835
    KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Measured Divided 2759.61 1.31442 2099.49
    STAM signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Squared Subtracted 86861.5 21491.8 65369.7
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Rooted Divided 54.9787 1.20486 66.2416
    140 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Squared 81527.6 1.45091 56190.6
    FLNB filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Rooted 55.6161 1.19989 66.7332
    HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Measured Subtracted 2597.5 1899 698.5
    KCNIP2 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Divided 2760.28 1.31425 2100.27
    NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Ranked Subtracted 228.306 30.295 198.011
    PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Squared 86609.4 21374.9 65234.5
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Ranked Divided 59 1.20408 49
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Rooted Subtracted 39.9725 13.0248 52.9973
    141 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared Divided 81520.8 1.45084 56188.5
    COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Ranked Subtracted 239.991 29.247 269.238
    HBS1L hbs1-like. [refseq;acc:nm_006620] Measured 2597.5 1899 698.5
    PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Squared 86600.9 21371 65229.9
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Rooted Divided 55.6161 1.19989 66.7332
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Ranked 59 1.20408 49
    SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Measured 4405.4 1.3125 5782.08
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Rooted Subtracted 105.205 12.9635 92.2415
    142 CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Squared Divided 81478.9 1.45044 56175.2
    CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted Subtracted 105.205 12.9635 92.2415
    JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 1885.19 7523.39
    PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Divided 9276.47 1.30832 7090.37
    PPIB peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Squared Subtracted 86600.9 21371 65229.9
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Rooted Divided 55.6161 1.19989 66.7332
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Ranked 59 1.20408 49
    THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 239.99 29.244 269.234
    143 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured Divided 9275.1 1.30826 7089.65
    ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Ranked 59 1.20408 49
    CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Measured Subtracted 15427.2 1854.4 13572.8
    OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Squared 86600.9 21371 65229.9
    PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Divided 124319 1.43145 86848.2
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted 55.6161 1.19989 66.7332
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked Subtracted 240.133 28.751 211.382

    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/