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 Hugo Value Type description Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1101 to 1150 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    138 MSI1 Rooted musashi 1. [refseq;acc:nm_002442] High confidence 1.20486 54.9787 66.2416
    PPP2CA Ranked serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 1.20493 194.372 234.204
    UBAC1 Squared putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 1.45156 468498 322755
    ZFAND6 protein associated with prk1. [refseq;acc:nm_019006] Low confidence 1.13346 79152.9 69833.1
    139 no value Measured 60s ribosomal protein l37a. [swissprot;acc:p12751] 1.08946 5762.4 6277.91
    APBA1 Ranked 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] High confidence 1.20415 271.752 225.68
    ARHGEF6 Rooted rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 1.07028 65.9882 70.626
    CCNB2 Squared g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] High confidence 1.45153 81592.1 56211.1
    KCNIP4 Measured potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 1.31442 2759.61 2099.49
    PPP1R7 Squared protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Low confidence 1.13344 60231.9 53140.7
    SPOCK1 Ranked testican-1 precursor (spock protein). [swissprot;acc:q08629] 1.06291 220.254 234.111
    ZC3H14 Rooted nuclear protein ukp68. [refseq;acc:nm_024824] High confidence 1.20486 54.9787 66.2416
    140 no value putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Low confidence 1.07022 69.4376 64.8818
    CDK2 Squared cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] High confidence 1.45091 81527.6 56190.6
    FLNB Rooted 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] 1.19989 55.6161 66.7332
    KCNIP2 Measured 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] 1.31425 2760.28 2100.27
    RRAGA Ranked ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 1.20408 59 49
    SLC16A5 Squared monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] Low confidence 1.13186 62486.3 70725.6
    SPOCK2 Ranked testican-2 precursor. [swissprot;acc:q92563] 1.06278 220.222 234.047
    UBE1C Measured ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] 1.08944 7628.44 8310.74
    141 ARHGEF7 Ranked rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 1.0621 219.344 206.52
    CCNB1 Squared g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] High confidence 1.45084 81520.8 56188.5
    DAZAP1 Rooted daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Low confidence 1.07004 65.6112 70.2066
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] High confidence 1.19989 55.6161 66.7332
    RRAGC Ranked ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 1.20408 59 49
    SLC16A1 Squared monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Low confidence 1.13172 62462.2 70689.7
    SNRPD2 Measured small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] High confidence 1.3125 4405.4 5782.08
    T brachyury protein (t protein). [swissprot;acc:o15178] Low confidence 1.08897 6171.76 6720.84
    142 CDC2 Squared cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] High confidence 1.45044 81478.9 56175.2
    MAN1B1 Ranked endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Low confidence 1.06201 211.056 198.732
    OTC Measured ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 1.08837 10803 11757.7
    PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] High confidence 1.30832 9276.47 7090.37
    PRMT1 Rooted protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 1.19989 55.6161 66.7332
    PROM1 prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Low confidence 1.07004 65.6112 70.2066
    RRAGB Ranked ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] High confidence 1.20408 59 49
    SLC16A7 Squared monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Low confidence 1.13166 62451.1 70673.1
    143 no value Rooted ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 1.06952 71.2143 76.1654
    ALG1 Measured beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] High confidence 1.30826 9275.1 7089.65
    ANLN Ranked anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 1.20408 59 49
    HAAO Measured 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Low confidence 1.08815 10696.6 11639.5
    PPP1R13B Squared protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] High confidence 1.43145 124319 86848.2
    PRMT8 Rooted protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 1.19989 55.6161 66.7332
    PSEN2 Ranked presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Low confidence 1.06201 211.056 198.732
    SLC16A8 Squared monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] 1.13144 62413.6 70617.4
    144 ARRB2 Measured beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 1.08814 7692.29 8370.25
    FBXW7 Ranked f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 1.06201 211.056 198.732
    KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 1.20312 265.686 319.651
    RPS6KC1 Rooted ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Low confidence 1.06928 71.2226 76.1572
    SLC16A3 Squared monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] 1.13076 62293.5 70439
    SNRP70 Rooted u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] High confidence 1.19989 55.6161 66.7332

    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/