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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3218 to 3267 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1609 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Divided 208.113 204.876 1.0158
1610 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Subtracted 217.446 214.2 3.246
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Divided 208.122 204.886 1.01579
1611 p10-binding protein. [refseq;acc:nm_024491] 221.313 217.877 1.01577
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Subtracted 217.446 214.2 3.246
1612 enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Divided 221.426 224.902 1.0157
pp1201 protein. [refseq;acc:nm_022152] Subtracted 217.446 214.2 3.246
1613 hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Divided 182.378 185.241 1.0157
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted 217.446 214.2 3.246
1614 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Divided 217.233 213.897 1.0156
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Subtracted 217.446 214.2 3.246
1615 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Divided 246.38 242.596 1.0156
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Subtracted 217.446 214.2 3.246
1616 n-acetylglutamate synthase. [refseq;acc:nm_153006] Divided 223.179 226.611 1.01538
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Subtracted 208.106 204.867 3.239
1617 serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Divided 221.045 217.699 1.01537
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Subtracted 208.113 204.876 3.237
1618 transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] Divided 227.768 231.246 1.01527
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Subtracted 208.122 204.886 3.236
1619 survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] 228.496 231.729 3.233
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Divided 227.768 231.246 1.01527
1620 ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Subtracted 228.496 231.729 3.233
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Divided 228.611 225.185 1.01521
1621 ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Subtracted 228.496 231.729 3.233
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Divided 228.611 225.185 1.01521
1622 nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769]
nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426] Subtracted 228.496 231.729 3.233
1623 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Divided 228.611 225.185 1.01521
ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153] Subtracted 228.496 231.729 3.233
1624 dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992]
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Divided 230.643 227.194 1.01518
1625 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 217.446 214.2 1.01515
survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] Subtracted 228.496 231.729 3.233
1626 probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6]
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Divided 217.446 214.2 1.01515
1627 pp1201 protein. [refseq;acc:nm_022152]
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Subtracted 220.686 217.481 3.205
1628 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 196.215 193.018 3.197
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Divided 217.446 214.2 1.01515
1629 pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Subtracted 196.192 192.996 3.196
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Divided 217.446 214.2 1.01515
1630 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Subtracted 196.192 192.996 3.196
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Divided 217.446 214.2 1.01515
1631 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 218.789 215.533 1.01511
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Subtracted 196.192 192.996 3.196
1632 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 196.191 3.195
mitotic checkpoint protein bub3. [swissprot;acc:o43684] Divided 221.934 218.658 1.01498
1633 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Subtracted 196.171 192.977 3.194
zinc finger protein 207. [swissprot;acc:o43670] Divided 221.934 218.658 1.01498
1634 hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Subtracted 219.745 222.928 3.183

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
- 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/