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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1286 to 1335 of 66312 in total
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
Interaction Map
red
network_comparison
green
81 CCNG2 cyclin g2. [swissprot;acc:q16589] Divided Squared High confidence 117718 1.66962 70505.9
EIF4B eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Rooted Low confidence 68.7629 1.0978 75.4877
HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Subtracted Ranked High confidence 252.371 50.355 202.016
NDN necdin. [swissprot;acc:q99608] Measured Low confidence 11285.3 966.8 10318.5
PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Divided Rooted High confidence 63.7475 1.32362 48.1615
RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted Ranked Low confidence 247.087 18.394 228.693
RGS12 regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Divided Measured 5528.68 1.11183 6146.97
RHBDL1 rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783] Squared 281799 1.23446 228277
TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Ranked 227.623 1.09286 208.281
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Measured High confidence 4136.36 1.43691 5943.56
ZNF547 sedlin. [swissprot;acc:o14582] Subtracted Squared 112820 44213 157033
82 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Low confidence 60811 10343.7 50467.3
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 112820 44213 157033
ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Divided Rooted 60.8022 1.30768 79.5099
CCNG1 cyclin g1 (cyclin g). [swissprot;acc:p51959] Squared 117718 1.66962 70505.8
COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Subtracted Ranked 252.329 50.325 202.004
DGKH diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Divided Low confidence 226.981 1.09085 208.077
GMPPA gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Squared 75927.4 1.22949 61755.3
GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Ranked High confidence 267.636 1.25304 335.359
GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Subtracted Rooted 40.3337 16.0593 24.2744
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured 20446.1 3690.3 24136.4
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided Low confidence 7098.44 1.1108 7884.98
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted 11285.3 966.8 10318.5
SLC7A9 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Divided Rooted 68.7629 1.0978 75.4877
SMYD2 set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Subtracted 59.2532 6.8009 66.0541
SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided Measured High confidence 4172.91 1.42694 5954.48
TAF2 tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] Subtracted Ranked Low confidence 237.567 18.338 219.229
83 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 60759.9 10244.4 50515.5
DGKD diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Divided Ranked 226.981 1.09085 208.077
DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured 7030.67 1.10869 7794.8
FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] High confidence 4932.27 1.42597 7033.29
GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Subtracted Rooted 40.3357 16.0442 24.2915
HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 50.311 201.998
MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 88.2482 1.24949 110.265
MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Subtracted Measured Low confidence 11285.3 966.8 10318.5
NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Divided Squared 60583.7 1.22607 74280
PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Subtracted Measured High confidence 21644.2 3545.5 18098.7
PPP2R1B 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] Divided Rooted 63.6507 1.30666 48.7127
PPP2R5A 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] Squared 117718 1.66962 70505.9
SMYD1 set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Subtracted Rooted Low confidence 59.2532 6.8009 66.0541
STARD7 star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Divided 61.8872 1.09753 67.9229
Subtracted Ranked 228.743 17.979 210.764
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Squared High confidence 112820 44213 157033
84 no value jun dimerization protein. [refseq;acc:nm_130469] Divided Measured 4932.27 1.42597 7033.29
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked Low confidence 226.338 1.08882 207.874
Rooted 62.4962 1.09638 68.5193
BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Squared High confidence 117515 1.66896 70412.3
CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Subtracted Low confidence 82257.5 10135 72122.5
GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Rooted High confidence 40.3358 16.0439 24.2919
HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked 252.296 50.301 201.995

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/