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 1108 to 1157 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    277 RPL4 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Subtracted High confidence 239.277 262.434 23.157
    278 BEST2 vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Low confidence 37.9984 29.1831 8.8153
    MYEF2 myelin gene expression factor 2. [refseq;acc:nm_016132] High confidence 235.383 258.476 23.093
    RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 241.399 267.088 1.10642
    SLC7A10 asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82] Low confidence 205.006 196.369 1.04398
    279 BTBD14B transcriptional repressor nac1. [refseq;acc:nm_052876] 202.309 211.2 1.04395
    GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Subtracted 210.132 201.397 8.735
    PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] High confidence 242.66 265.715 23.055
    RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided 252.644 228.42 1.10605
    280 LAPTM4B lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] Subtracted Low confidence 210 201.325 8.675
    MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] Divided High confidence 252.512 228.356 1.10578
    TFCP2L1 lbp-9. [refseq;acc:nm_014553] Low confidence 219.758 210.509 1.04394
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted High confidence 267.208 244.168 23.04
    281 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 241.808 267.335 1.10557
    MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Subtracted 242.159 265.104 22.945
    TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Divided Low confidence 219.749 210.503 1.04392
    TMEM115 pl6 protein (placental protein 6). [swissprot;acc:q12893] Subtracted 209.995 201.322 8.673
    282 AMY1C alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] Divided 219.742 210.498 1.04391
    LAPTM4A lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] Subtracted 209.995 201.322 8.673
    NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] High confidence 242.159 265.104 22.945
    RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Divided 252.39 228.297 1.10553
    283 KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Subtracted Low confidence 209.31 200.66 8.65
    MRPL11 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] High confidence 242.37 265.255 22.885
    RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Divided 241.828 267.346 1.10552
    UBP1 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Low confidence 219.722 210.484 1.04389
    284 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] High confidence 224.657 203.235 1.10541
    POLR3A dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Subtracted 242.686 265.516 22.83
    SLC7A10 asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82] Low confidence 205.006 196.369 8.637
    TNKS2 tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [swissprot;acc:q9h2k2] Divided 214.675 205.692 1.04367
    285 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 224.647 203.242 1.10532
    POLR1A dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Subtracted 242.691 265.481 22.79
    TAF4 transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Divided Low confidence 202.354 211.175 1.04359
    TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Subtracted 201.219 192.595 8.624
    286 HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 210.057 201.45 8.607
    NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Divided High confidence 224.633 203.251 1.1052
    RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] Subtracted 242.593 265.365 22.772
    TAF4B transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] Divided Low confidence 202.356 211.174 1.04358
    287 GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 210.132 201.397 1.04337
    HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Subtracted 210.05 201.454 8.596
    RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Divided High confidence 240.758 266.079 1.10517
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Subtracted 225.217 202.459 22.758
    288 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Divided 240.758 266.078 1.10517
    DICER1 endoribonuclease dicer (ec 3.1.26.-) (helicase with rnase motif) (helicase-moi). [swissprot;acc:q9upy3] Subtracted Low confidence 208.915 200.322 8.593
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 200.288 192.004 1.04314
    STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Subtracted High confidence 234.691 257.442 22.751
    289 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Divided 272.781 246.892 1.10486
    DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Subtracted Low confidence 57.395 48.8186 8.5764
    KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 209.31 200.66 1.04311
    STX6 syntaxin 6. [swissprot;acc:o43752] Subtracted High confidence 234.673 257.414 22.741
    290 no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 242.109 264.79 22.681

    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/