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 658 to 707 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    83 Measured 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
    Ranked melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] High confidence no value 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] Low confidence KCND2 1.08671 225.735 245.308
    Squared autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] High confidence ATG12 1.65709 67438.6 40697
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Low confidence no value 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] High confidence NFYA 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] Low confidence DFFB 1.09453 61.1174 66.8946
    86 Measured protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] High confidence FOSB 1.42384 4942.49 7037.32
    vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Low confidence PTPRA 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] High confidence MAGEA11 1.24949 88.2482 110.265
    Squared septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Low confidence SEPT7 1.2051 66860.1 80573.4
    transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] High confidence KRAS 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] Low confidence BACH1 1.09372 79.2778 86.7076
    87 Measured fos-related antigen 1 (fra-1). [swissprot;acc:p15407] High confidence FOSL1 1.42347 4944.3 7038.04
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Low confidence DVL3 1.10707 7054.1 7809.38
    Ranked melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] High confidence MAGEA2B 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] Low confidence KCND3 1.08596 225.545 244.933
    Squared gaba-a receptor-associated protein. [sptrembl;acc:q9by60] no value 1.20496 60811 50467.3
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] High confidence SHOC2 1.64464 105482 64136.9
    Rooted 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] APBA1 1.30003 42.2825 54.9687
    nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] Low confidence NFE2L2 1.09372 79.2778 86.7076
    88 Measured potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence KCND2 1.42259 2411.93 1695.45
    serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Low confidence MAK 1.10399 9631.47 10633
    Ranked hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] High confidence no value 1.24949 88.2482 110.265
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Low confidence KCND1 1.0855 225.428 244.701
    Squared apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 1.2028 60759.9 50515.5
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] High confidence no value 1.64463 105482 64137.2
    Rooted presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] PSEN2 1.29795 37.3005 48.4141
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Low confidence BACH2 1.09372 79.2778 86.7076
    89 Measured cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] High confidence CTH 1.4217 2414.22 1698.12
    intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Low confidence ICK 1.10368 9623.55 10621.3
    Ranked melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] High confidence MAGEA6 1.24949 88.2482 110.265

    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/