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 [...,...].
    Network Comparison Type Rank Gene Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 625 to 674 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    79 Measured ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Low confidence FCN2 1.11235 5334.13 5933.4
    protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence UFC1 1.48558 3074.57 4567.51
    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] Low confidence APBA1 1.09742 229.144 208.803
    voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] High confidence CACNG3 1.2567 254.693 202.668
    Squared raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 1.67005 117850 70566.8
    rhomboid-related protein 4 (ec 3.4.21.-) (ventrhoid transmembrane protein). [swissprot;acc:p58872] Low confidence RHBDL3 1.23446 281799 228277
    Rooted cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] SLC7A11 1.0978 68.7629 75.4877
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] High confidence no value 1.3237 63.7477 48.1588
    80 Measured nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 1.43834 4133.47 5945.32
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Low confidence no value 1.11235 5334.13 5933.4
    Ranked rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 1.09499 221.194 202.005
    voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] High confidence CACNG4 1.25669 254.691 202.668
    Squared bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] Low confidence TEGT 1.23446 281799 228277
    serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] High confidence PPP2R5E 1.66962 117718 70505.9
    Rooted serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] PPP2R2B 1.32368 63.7477 48.1594
    solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Low confidence SLC7A6 1.0978 68.7629 75.4877
    81 Measured nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] High confidence TIAL1 1.43691 4136.36 5943.56
    regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Low confidence RGS12 1.11183 5528.68 6146.97
    Ranked transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] TFDP2 1.09286 227.623 208.281
    voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] High confidence CACNG5 1.25645 254.614 202.646
    Squared cyclin g2. [swissprot;acc:q16589] CCNG2 1.66962 117718 70505.9
    rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783] Low confidence RHBDL1 1.23446 281799 228277
    Rooted eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] EIF4B 1.0978 68.7629 75.4877
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] High confidence PPP2R2C 1.32362 63.7475 48.1615
    82 Measured lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Low confidence LASS2 1.1108 7098.44 7884.98
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] High confidence SNRPD1 1.42694 4172.91 5954.48
    Ranked diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Low confidence DGKH 1.09085 226.981 208.077
    guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence GNB5 1.25304 267.636 335.359
    Squared cyclin g1 (cyclin g). [swissprot;acc:p51959] CCNG1 1.66962 117718 70505.8
    gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Low confidence GMPPA 1.22949 75927.4 61755.3
    Rooted b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] SLC7A9 1.0978 68.7629 75.4877
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence ATF3 1.30768 60.8022 79.5099
    83 Measured proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] FOS 1.42597 4932.27 7033.29
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Low confidence DVL1 1.10869 7030.67 7794.8
    Ranked diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] DGKD 1.09085 226.981 208.077
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] High confidence MAGED4 1.24949 88.2482 110.265
    Squared hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Low confidence NFU1 1.22607 60583.7 74280
    serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] High confidence PPP2R5A 1.66962 117718 70505.9
    Rooted serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] PPP2R1B 1.30666 63.6507 48.7127
    star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Low confidence STARD7 1.09753 61.8872 67.9229
    84 Measured jun dimerization protein. [refseq;acc:nm_130469] High confidence no value 1.42597 4932.27 7033.29
    septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Low confidence SEPT4 1.10857 11141.5 12351.1
    Ranked hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] High confidence MAGEE2 1.24949 88.2482 110.265
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Low confidence no value 1.08882 226.338 207.874
    Squared b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] High confidence BRAF 1.66896 117515 70412.3
    nucleolin (protein c23). [swissprot;acc:p19338] Low confidence NCL 1.20735 70162 58112.6
    Rooted 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] High confidence NFYC 1.30362 46.7419 60.9337
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Low confidence no value 1.09638 62.4962 68.5193
    85 Measured fos-related antigen 2. [swissprot;acc:p15408] High confidence FOSL2 1.42395 4941.95 7037.11
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence DVL2 1.10843 7034.43 7797.14

    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/