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 544 to 593 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    136 NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Measured 3620.77 4763.34 1.31556
    137 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared 81606.8 56215.8 1.45167
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Rooted 54.9787 66.2416 1.20486
    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 3620.77 4763.34 1.31556
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked 350 290 1.2069
    138 KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Measured 2755.15 2094.3 1.31555
    MSI1 musashi 1. [refseq;acc:nm_002442] Rooted 54.9787 66.2416 1.20486
    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 194.372 234.204 1.20493
    UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Squared 468498 322755 1.45156
    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 271.752 225.68 1.20415
    CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Squared 81592.1 56211.1 1.45153
    KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Measured 2759.61 2099.49 1.31442
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Rooted 54.9787 66.2416 1.20486
    140 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Squared 81527.6 56190.6 1.45091
    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 66.7332 1.19989
    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] Measured 2760.28 2100.27 1.31425
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Ranked 59 49 1.20408
    141 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared 81520.8 56188.5 1.45084
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Rooted 55.6161 66.7332 1.19989
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Ranked 59 49 1.20408
    SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Measured 4405.4 5782.08 1.3125
    142 CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Squared 81478.9 56175.2 1.45044
    PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Measured 9276.47 7090.37 1.30832
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Rooted 55.6161 66.7332 1.19989
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Ranked 59 49 1.20408
    143 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured 9275.1 7089.65 1.30826
    ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Ranked 59 49 1.20408
    PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Squared 124319 86848.2 1.43145
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted 55.6161 66.7332 1.19989
    144 KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Ranked 265.686 319.651 1.20312
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 66.7332 1.19989
    TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Squared 123324 86277.9 1.42938
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Measured 3349.9 4362.61 1.30231
    145 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Rooted 55.6161 66.7332 1.19989
    nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Squared 310840 442993 1.42515
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 16771.5 12889.1 1.30122
    KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked 265.639 319.546 1.20293
    146 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] 265.632 319.531 1.20291
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Rooted 55.0737 66.0298 1.19894
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Squared 103496 146848 1.41888
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Measured 11068 8508.5 1.30082
    147 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Ranked 50.7983 42.3003 1.2009
    CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Measured 11068 8508.5 1.30082
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Rooted 42.0574 50.4237 1.19893
    RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Squared 103496 146848 1.41888
    148 FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Rooted 42.0577 50.424 1.19892
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Squared 103496 146848 1.41888
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Measured 11068 8508.5 1.30082
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Ranked 296.677 247.559 1.19841
    149 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718

    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/