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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Hugo measured Gene Rank expected description final
Results: HTML CSV LaTeX Showing element 951 to 1000 of 3206 in total
Hugo
measured
Rank
expected
description
final
CTSL2 0.163807 1035 0.646587 CATHEPSIN L2 PRECURSOR (EC 3.4.22.43) (CATHEPSIN V) (CATHEPSIN U). [SWISSPROT;Acc:O60911] 0.253341004
CUEDC2 0.139984 2472 0.646308 0.216590233
CUGBP1 0.267337 548 0.986471 CUG TRIPLET REPEAT RNA-BINDING PROTEIN 1 (CUG-BP1) (RNA-BINDING PROTEIN BRUNOL-2) (DEADENYLATION FACTOR CUG-BP) (50 KDA NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN) (EDEN-BP). [SWISSPROT;Acc:Q92879] 0.271003405
CUGBP2 0.24526 547 0.905006 "CUG TRIPLET REPEAT, RNA BINDING PROTEIN 2; ELAV-TYPE RNA-BINDING PROTEIN; CUG TRIPLET REPEAT,RNA-BINDING PROTEIN 2; CUG TRIPLET REPEAT, RNA-BINDING PROTEIN 2; NEUROBLASTOMA APOPTOSIS-RELATED RNA-BINDING PROTEIN. [RefSeq;Acc:NM_006561]" 0.271003728
CUL1 0.0313105 3179 0.629022 CULLIN HOMOLOG 1 (CUL-1). [SWISSPROT;Acc:Q13616] 0.049776478
CUL2 0.0241952 3181 0.486077 CULLIN HOMOLOG 2 (CUL-2). [SWISSPROT;Acc:Q13617] 0.049776476
CUTL1 0.187173 41 0.444789 CCAAT DISPLACEMENT PROTEIN (CDP) (CUT-LIKE 1). [SWISSPROT;Acc:P39880] 0.420813015
CUTL2 0.147881 42 0.35143 HOMEOBOX PROTEIN CUX-2 (CUT-LIKE 2) (FRAGMENT). [SWISSPROT;Acc:O14529] 0.420797883
CWF19L2 0.0315866 1930 0.136317 0.231714313
CXorf56 0.0513128 2880 0.278146 0.184481531
CXXC1 0.0439174 989 0.172112 CPG BINDING PROTEIN (PROTEIN CONTAINING PHD FINGER AND CXXC DOMAIN 1). [SWISSPROT;Acc:Q9P0U4] 0.255167565
CYB5D2 0.0411817 1156 0.164951 0.249660202
CYB5R1 0.11223 2200 0.497084 CYTOCHROME B5 REDUCTASE 1 (B5R.1). [RefSeq;Acc:NM_016243] 0.22577673
CYB5R2 0.112427 2199 0.497956 CYTOCHROME B5 REDUCTASE B5R.2. [RefSeq;Acc:NM_016229] 0.225776976
CYB5R3 0.0966308 2201 0.427993 NADH-CYTOCHROME B5 REDUCTASE (EC 1.6.2.2) (B5R). [SWISSPROT;Acc:P00387] 0.22577659
CYC1 0.150184 1621 0.62682 "CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL PRECURSOR (CYTOCHROME C-1). [SWISSPROT;Acc:P08574]" 0.239596694
CYCS 0.0314533 1406 0.128904 CYTOCHROME C. [SWISSPROT;Acc:P00001] 0.244005617
CYLD 0.0366317 1256 0.148106 "CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [RefSeq;Acc:NM_015247]" 0.247334342
CYP2D6 0.0555486 2520 0.258646 CYTOCHROME P450 2D6 (EC 1.14.14.1) (CYPIID6) (P450-DB1) (DEBRISOQUINE 4-HYDROXYLASE). [SWISSPROT;Acc:P10635] 0.214766901
CYP4A11 0.118945 632 0.443397 CYTOCHROME P450 4A11 PRECURSOR (EC 1.14.15.3) (CYPIVA11) (FATTY ACID OMEGA-HYDROXYLASE) (P-450 HK OMEGA) (LAURIC ACID OMEGA-HYDROXYLASE) (CYP4AII) (P450-HL-OMEGA). [SWISSPROT;Acc:Q02928] 0.268258468
CYP4A22 0.116014 636 0.432472 "DJ18D14.4 (CYTOCHROME P450, SUBFAMILY IVA, POLYPEPTIDE 11). [SPTREMBL;Acc:Q9NTL5]" 0.268257829
CYP4B1 0.0960386 627 0.358007 CYTOCHROME P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-HP). [SWISSPROT;Acc:P13584] 0.268259001
CYP4F11 0.113522 623 0.42318 CYTOCHROME P450 4F11 (EC 1.14.14.1) (CYPIVF11). [SWISSPROT;Acc:Q9HBI6] 0.26825937
CYP4F12 0.110995 634 0.413762 CYTOCHROME P450 4F12 (EC 1.14.14.1) (CYPIVF12). [SWISSPROT;Acc:Q9HCS2] 0.268258081
CYP4F2 0.118945 630 0.443397 CYTOCHROME P450 4F2 (EC 1.14.13.30) (CYPIVF2) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:P78329] 0.268258468
CYP4F22 0.102776 625 0.383122 0.268259197
CYP4F3 0.115475 637 0.430463 CYTOCHROME P450 4F3 (EC 1.14.13.30) (CYPIVF3) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:Q08477] 0.268257667
CYP4F8 0.118945 631 0.443397 CYTOCHROME P450 4F8 (EC 1.14.14.1) (CYPIVF8). [SWISSPROT;Acc:P98187] 0.268258468
CYP4X1 0.0954996 629 0.355998 LIKELY ORTHOLOG OF RAT CYTOCHROME P450 4X1. [RefSeq;Acc:NM_178033] 0.26825881
D2HGDH 0.256113 2337 1.15814 0.221141658
DAB2IP 0.0659913 3072 0.639469 DAB2 INTERACTING PROTEIN; NGAP-LIKE PROTEIN; DOC-2/DAB2 INTERACTIVE PROTEIN. [RefSeq;Acc:NM_032552] 0.103197028
DAD1 0.0621814 2122 0.272579 DEFENDER AGAINST CELL DEATH 1 (DAD-1). [SWISSPROT;Acc:P46966] 0.228122489
DAGLA 0.023532 1975 0.101818 0.23111827
DAGLB 0.0305909 1974 0.13236 KCCR13L. [RefSeq;Acc:NM_139179] 0.231118918
DARS 0.149127 2665 0.712692 ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12) (ASPARTATE--TRNA LIGASE) (ASPRS). [SWISSPROT;Acc:P14868] 0.209244667
DARS2 0.0841705 2035 0.365653 0.230192286
DAZAP1 0.0774957 651 0.289339 DAZ ASSOCIATED PROTEIN 1 ISOFORM B; DELETED IN AZOOSPERMIA ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_018959] 0.267837035
DBT 0.121426 1212 0.489504 "LIPOAMIDE ACYLTRANSFERASE COMPONENT OF BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.-) (E2) (DIHYDROLIPOAMIDE BRANCHED CHAIN TRANSACYLASE) (BCKAD E2 SUBUNIT). [SWISSPROT;Acc:P11182]" 0.24805926
DCAKD 0.208679 2310 0.939792 0.22204807
DCLK1 0.408607 1432 1.67671 SERINE/THREONINE-PROTEIN KINASE DCAMKL1 (EC 2.7.1.-) (DOUBLECORTIN- LIKE AND CAM KINASE-LIKE 1). [SWISSPROT;Acc:O15075] 0.24369569
DCLK2 0.352259 1425 1.44441 0.243877431
DCP1A 0.289798 2411 1.3266 TRANSCRIPTION FACTOR SMIF; DECAPPING ENZYME HDCP1A. [RefSeq;Acc:NM_018403] 0.218451681
DCPS 0.279017 2993 2.06166 MRNA DECAPPING ENZYME; HISTIDINE TRIAD PROTEIN MEMBER 5; HEAT SHOCK-LIKE PROTEIN 1. [RefSeq;Acc:NM_014026] 0.135336088
DCT 0.10083 1134 0.402579 DOPACHROME TAUTOMERASE PRECURSOR (EC 5.3.3.12) (DT) (DCT) (DOPACHROME DELTA-ISOMERASE) (TYROSINASE-RELATED PROTEIN 2) (TRP-2) (TRP2). [SWISSPROT;Acc:P40126] 0.250460158
DCTD 0.124149 2664 0.593022 DEOXYCYTIDYLATE DEAMINASE (EC 3.5.4.12) (DCMP DEAMINASE). [SWISSPROT;Acc:P32321] 0.209349737
DCTN2 0.375423 1694 1.57827 DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [SWISSPROT;Acc:Q13561] 0.237869946
DCTN5 0.0462274 1865 0.198227 DYNACTIN 4. [RefSeq;Acc:NM_032486] 0.233204357
DCX 0.303311 1401 1.24261 DOUBLECORTIN (LISSENCEPHALIN-X) (LIS-X) (DOUBLIN). [SWISSPROT;Acc:O43602] 0.244091871
DDB1 0.0761267 1108 0.303457 DNA DAMAGE BINDING PROTEIN 1 (DAMAGE-SPECIFIC DNA BINDING PROTEIN 1) (DDB P127 SUBUNIT) (DDBA) (UV-DAMAGED DNA-BINDING PROTEIN 1) (UV-DDB 1) (XERODERMA PIGMENTOSUM GROUP E COMPLEMENTING PROTEIN) (XPCE) (X- ASSOCIATED PROTEIN 1) (XAP-1). [SWISSPROT; 0.250864867
DDI1 0.0624093 1643 0.2611 0.239024512

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/