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 Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 644 to 693 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    81 Ranked voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] CACNG5 High confidence 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] RHBDL1 Low confidence 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] PPP2R2C High confidence 1.32362 63.7475 48.1615
    82 Measured lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 Low confidence 1.1108 7098.44 7884.98
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 High confidence 1.42694 4172.91 5954.48
    Ranked diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] DGKH Low confidence 1.09085 226.981 208.077
    guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] GNB5 High confidence 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] GMPPA Low confidence 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] ATF3 High confidence 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] DVL1 Low confidence 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] MAGED4 High confidence 1.24949 88.2482 110.265
    Squared hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 Low confidence 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] PPP2R5A High confidence 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] STARD7 Low confidence 1.09753 61.8872 67.9229
    84 Measured jun dimerization protein. [refseq;acc:nm_130469] no value High confidence 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] SEPT4 Low confidence 1.10857 11141.5 12351.1
    Ranked hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2 High confidence 1.24949 88.2482 110.265
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] no value Low confidence 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] BRAF High confidence 1.66896 117515 70412.3
    nucleolin (protein c23). [swissprot;acc:p19338] NCL Low confidence 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] NFYC High confidence 1.30362 46.7419 60.9337
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] no value Low confidence 1.09638 62.4962 68.5193
    85 Measured fos-related antigen 2. [swissprot;acc:p15408] FOSL2 High confidence 1.42395 4941.95 7037.11
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] DVL2 Low confidence 1.10843 7034.43 7797.14
    Ranked melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] no value High confidence 1.24949 88.2482 110.265
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] KCND2 Low confidence 1.08671 225.735 245.308
    Squared autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] ATG12 High confidence 1.65709 67438.6 40697
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] no value Low confidence 1.20712 60862.1 50419.2
    Rooted 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] NFYA High confidence 1.30362 46.7419 60.9337
    dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] DFFB Low confidence 1.09453 61.1174 66.8946
    86 Measured protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB High confidence 1.42384 4942.49 7037.32
    vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] PTPRA Low confidence 1.10773 7263.76 8046.29
    Ranked dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] DFFB 1.08645 233.922 215.309
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 High confidence 1.24949 88.2482 110.265
    Squared septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7 Low confidence 1.2051 66860.1 80573.4
    transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] KRAS High confidence 1.64468 105500 64146.3
    Rooted serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] PPP2R1A 1.30146 63.6205 48.8838
    transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] BACH1 Low confidence 1.09372 79.2778 86.7076
    87 Measured fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 High confidence 1.42347 4944.3 7038.04
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 Low confidence 1.10707 7054.1 7809.38
    Ranked melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] MAGEA2B High confidence 1.24949 88.2482 110.265
    potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] KCND3 Low confidence 1.08596 225.545 244.933
    Squared gaba-a receptor-associated protein. [sptrembl;acc:q9by60] no value 1.20496 60811 50467.3

    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/