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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 477 to 526 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    120 HMG20B Measured high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 5136.78 6895.98 1.34247
    HOMER1 Rooted homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 50.3333 62.9942 1.25154
    KCND2 Ranked potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 269.278 327.709 1.21699
    PAPOLG Squared poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 210199 136638 1.53836
    121 CTH Ranked cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 327.655 1.2169
    HOMER3 Rooted homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 50.339 62.9975 1.25147
    JUNB Measured transcription factor jun-b. [swissprot;acc:p17275] 5579.18 7488.4 1.3422
    PPP1CC Squared serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 199594 130021 1.53509
    122 CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 201896 131906 1.53061
    HMG20A Measured high-mobility group 20a. [refseq;acc:nm_018200] 5140.14 6893.53 1.34112
    JUND Rooted transcription factor jun-d. [swissprot;acc:p17535] 63.636 79.6225 1.25122
    KCND3 Ranked 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] 269.248 327.642 1.21688
    123 ATG4A Measured cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 24260.3 18172.1 1.33503
    KCND1 Ranked potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 269.23 327.601 1.21681
    PPP1R2 Squared protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 192904 126167 1.52896
    TIA1 Rooted nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 54.6527 67.9743 1.24375
    124 HMG20B Ranked high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 208.52 171.595 1.21519
    MAP1LC3B Measured microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 24255.7 18168.9 1.33501
    PPP1R2P9 Squared type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 192779 126095 1.52884
    TIAL1 Rooted nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 54.6625 67.9477 1.24304
    125 HMG20A Ranked high-mobility group 20a. [refseq;acc:nm_018200] 208.588 171.778 1.21429
    MAP1LC3A Measured microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 24255.7 18168.9 1.33501
    RRS1 Squared ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 189976 124480 1.52616
    SNRPD1 Rooted small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 54.8203 67.934 1.23921
    126 ATG4B Measured cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 24250 18164.9 1.33499
    HMG20B Rooted high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 60.9342 75.1387 1.23311
    PPP1CA Squared serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 189976 124480 1.52616
    STAMBPL1 Ranked associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 94 114 1.21277
    127 no value Squared cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 88432.6 58423.3 1.51365
    CHMP2A Ranked putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 94 114 1.21277
    HMG20A Rooted high-mobility group 20a. [refseq;acc:nm_018200] 60.9353 75.094 1.23236
    JUND Measured transcription factor jun-d. [swissprot;acc:p17535] 5638.2 7523.39 1.33436
    128 no value Squared pnas-18. [sptrembl;acc:q9bzu3] 87787.3 58155.8 1.50952
    LUC7L2 Measured luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 4355.61 5810.82 1.3341
    STAMBP Ranked associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 94 114 1.21277
    TARDBP Rooted tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 48.0515 39.0445 1.23069
    129 LUC7L Measured luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 4358.13 5811.49 1.33348
    NCBP2L Rooted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 54.2343 66.7323 1.23044
    PCF11 Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 178263 118639 1.50257
    VPS24 Ranked neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 94 114 1.21277
    130 no value Rooted formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 55.1026 67.5701 1.22626
    C10orf83 Squared 44050 protein. [refseq;acc:nm_178832] 148058 99628.4 1.4861
    CHMP4A Ranked protein hspc134 (protein cda04). [swissprot;acc:q9by43] 94 114 1.21277
    FOXP4 Measured forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 2234.68 2978.53 1.33287
    131 no value Rooted huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 55.1113 67.5537 1.22577
    FOXP1 Measured forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 2234.73 2978.57 1.33285
    PPP1R8 Squared nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] 148058 99628.4 1.4861
    SON Ranked son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] 294.053 242.562 1.21228
    132 ATG5 Squared autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 36359.2 24466.8 1.48606
    FOXP3 Measured forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 2236.61 2980.35 1.33253

    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/