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.


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

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/