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.


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 1577 to 1626 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
1577 AMMECR1 ammecr1 protein. [refseq;acc:nm_015365] 222.585 218.982 1.01645
1578 RAE1 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]
1579 TATDN1 cda11 protein. [refseq;acc:nm_032026] 213.181 209.732 1.01644
1580 CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 168.018 170.769 1.01637
1581 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 168.002 170.753
1582 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 168.098 170.844 1.01634
1583 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 168.091 170.837
1584 PGLS 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 216.891 220.432 1.01633
1585 CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 168.145 170.888 1.01631
1586 AP1B1 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] 222.166 225.79
1587 C20orf4 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] 220.129 216.598 1.0163
1588 RNF25 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] 177.834 180.725 1.01626
1589 VARS valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] 223.589 227.219 1.01624
1590 TYMS thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] 225.119 228.769 1.01621
1591 no value dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
1592 SDF2 stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470]
1593 SDF2L1 stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
1594 JPH4 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 222.133 225.731 1.0162
1595 no value adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 222.134 1.01619
1596 AP1G1 adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747]
1597 AP1S3 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3]
1598 AP1S1 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382]
1599 DTNBP1 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 217.871 214.404 1.01617
1600 AP2B1 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] 222.103 225.675 1.01608
1601 PMM2 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 217.268 213.842 1.01602
1602 PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 217.334 213.914 1.01599
1603 no value heat shock factor binding protein 1. [swissprot;acc:o75506] 216.62 213.22 1.01595
1604 CLK2 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] 214.984 211.614 1.01593
1605 FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 217.322 213.916 1.01592
1606 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 207.916 204.662 1.0159
1607 CLK3 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] 214.982 211.622 1.01588
1608 TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 208.106 204.867 1.01581
1609 UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 208.113 204.876 1.0158
1610 UBE2V2 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] 208.122 204.886 1.01579
1611 CEP70 p10-binding protein. [refseq;acc:nm_024491] 221.313 217.877 1.01577
1612 no value enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] 221.426 224.902 1.0157
1613 HTATIP2 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] 182.378 185.241
1614 FOXA2 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 217.233 213.897 1.0156
1615 POLE2 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 246.38 242.596
1616 NAGS n-acetylglutamate synthase. [refseq;acc:nm_153006] 223.179 226.611 1.01538
1617 SHMT1 serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] 221.045 217.699 1.01537
1618 TCEA2 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] 227.768 231.246 1.01527
1619 no value transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]
1620 GTF2B transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] 228.611 225.185 1.01521
1621 ZNHIT3 thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]
1622 NHP2L1 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]
1623 NUFIP1 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]
1624 PDCD11 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] 230.643 227.194 1.01518
1625 RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 217.446 214.2 1.01515
1626 TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]

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/