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