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:
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expected Rank Gene description measured final Hugo
Results: HTML CSV LaTeX Showing element 1552 to 1601 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.504965 567 0.136702 0.270715792 DHRS7B
0.505165 82 TRANSCRIPTION FACTOR E2F1 (E2F-1) (RETINOBLASTOMA BINDING PROTEIN 3) (RBBP-3) (PRB-BINDING PROTEIN E2F-1) (PBR3) (RETINOBLASTOMA-ASSOCIATED PROTEIN 1) (RBAP-1). [SWISSPROT;Acc:Q01094] 0.198685 0.393307137 E2F1
0.505621 2032 0.116403 0.23021789 no value
0.506093 113 "SWI/SNF-RELATED, MATRIX-ASSOCIATED, ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY F MEMBER 1 (SWI-SNF COMPLEX PROTEIN P270) (B120). [SWISSPROT;Acc:O14497]" 0.182783 0.361164845 ARID1A
114 PROGRAMMED CELL DEATH PROTEIN 6 (PROBABLE CALCIUM-BINDING PROTEIN ALG- 2). [SWISSPROT;Acc:O75340] PDCD6
0.506251 1038 RETINOBLASTOMA-LIKE PROTEIN 1 (107 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB1) (P107). [SWISSPROT;Acc:P28749] 0.128252 0.253336784 RBL1
0.5063 889 NEURONAL KINESIN HEAVY CHAIN (NKHC) (KINESIN HEAVY CHAIN ISOFORM 5A) (KINESIN HEAVY CHAIN NEURON-SPECIFIC 1). [SWISSPROT;Acc:Q12840] 0.131576 0.259877543 KIF5A
0.506388 147 DELTEX HOMOLOG 1; HDX-1. [RefSeq;Acc:NM_004416] 0.177901 0.351313617 DTX1
0.50755 2251 "GLYCEROL-3-PHOSPHATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.1.99.5) (GPD-M) (GPDH-M). [SWISSPROT;Acc:P43304]" 0.113261 0.223152399 GPD2
0.508241 1155 0.126888 0.249661086 PAPLN
0.509096 1524 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M1 CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE LARGE CHAIN). [SWISSPROT;Acc:P23921] 0.123369 0.242329541 RRM1
0.509937 1465 MEIOTIC RECOMBINATION PROTEIN SPO11. [SWISSPROT;Acc:Q9Y5K1] 0.12393 0.243030021 SPO11
0.510598 2960 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [SWISSPROT;Acc:O15211] 0.0746316 0.146165085 no value
0.511852 448 0.141581 0.276605347 SEC16A
0.512059 1161 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 CL 0.127791 0.249563039 no value
0.513743 2806 ZINC FINGER PROTEIN 288 (DENDRITIC-DERIVED BTB/POZ ZINC FINGER PROTEIN). [SWISSPROT;Acc:Q9HC78] 0.101567 0.197700017 ZBTB20
0.514211 1645 UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG B (HHR23B) (XP-C REPAIR COMPLEMENTING COMPLEX 58 KDA PROTEIN) (P58). [SWISSPROT;Acc:P54727] 0.122909 0.239024447 RAD23B
0.514239 2409 0.112482 0.218734868 no value
0.514271 916 VACUOLAR PROTEIN SORTING 33A (HVPS33A). [SWISSPROT;Acc:Q96AX1] 0.132652 0.257941824 VPS33A
0.514373 2807 0.101691 0.197698946 no value
0.514942 2846 "RED CELL ACID PHOSPHATASE 1, ISOZYME F (EC 3.1.3.2) (ACP1) (LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE) (EC 3.1.3.48) (ADIPOCYTE ACID PHOSPHATASE, ISOZYME ALPHA). [SWISSPROT;Acc:P24666]" 0.0987604 0.191789367 ACP1
0.514965 948 RAB ACCEPTOR 1 (PRENYLATED); PRENYLATED RAB ACCEPTOR 1. [RefSeq;Acc:NM_006423] 0.13204 0.256405775 RABAC1
0.51515 1002 "FUMARATE HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.2) (FUMARASE). [SWISSPROT;Acc:P07954]" 0.131317 0.25491022 FH
0.515188 2889 0.0926874 0.179909858 C9orf95
0.517345 3069 0.0533885 0.103197093 no value
0.517346 236 IMPORTIN BETA-3 SUBUNIT (KARYOPHERIN BETA-3 SUBUNIT) (RAN-BINDING PROTEIN 5). [SWISSPROT;Acc:O00410] 0.162809 0.314700413 RANBP5
0.517492 2687 EH-DOMAIN CONTAINING PROTEIN 3. [SWISSPROT;Acc:Q9NZN3] 0.107786 0.208285345 EHD3
0.517633 1233 POLYBROMO 1. [RefSeq;Acc:NM_018165] 0.128218 0.247700591 PBRM1
0.517685 3183 PRESENILIN 2 (PS-2) (STM-2) (E5-1) (AD3LP) (AD5). [SWISSPROT;Acc:P49810] 0.0257685 0.049776408 PSEN2
0.518618 1129 TYROSINASE PRECURSOR (EC 1.14.18.1) (MONOPHENOL MONOOXYGENASE) (TUMOR REJECTION ANTIGEN AB) (SK29-AB) (LB24-AB). [SWISSPROT;Acc:P14679] 0.129983 0.250633414 TYR
0.519559 2289 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 2 ISOFORM 1; TAK1-BINDING PROTEIN 2. [RefSeq;Acc:NM_015093] 0.11552 0.22234241 MAP3K7IP2
0.519607 83 TRANSCRIPTION FACTOR E2F2 (E2F-2). [SWISSPROT;Acc:Q14209] 0.204365 0.393306865 E2F2
0.522903 2230 DNA MISMATCH REPAIR PROTEIN MLH3 (MUTL PROTEIN HOMOLOG 3). [SWISSPROT;Acc:Q9UHC1] 0.117296 0.224316938 MLH3
0.523598 76 0.212647 0.406126456 C22orf9
0.524421 190 CRK-ASSOCIATED SUBSTRATE (P130CAS) (BREAST CANCER ANTI-ESTROGEN RESISTANCE 1 PROTEIN). [SWISSPROT;Acc:P56945] 0.17117 0.326398066 BCAR1
0.524861 689 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN (EC 2.7.1.123) (CAM-KINASE II GAMMA CHAIN) (CAM KINASE II GAMMA SUBUNIT) (CAMK-II GAMMA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q13555] 0.139426 0.265643666 CAMK2G
0.525053 2725 0.10808 0.205845886 no value
0.525483 523 "1,4-ALPHA-GLUCAN BRANCHING ENZYME (EC 2.4.1.18) (GLYCOGEN BRANCHING ENZYME) (BRANCHER ENZYME). [SWISSPROT;Acc:Q04446]" 0.142881 0.271904134 GBE1
0.525788 1205 ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488] 0.130571 0.248333929 ZNF593
0.525864 1453 0.127901 0.243220681 UTP18
0.526194 108 "NONSPECIFIC LIPID-TRANSFER PROTEIN, MITOCHONDRIAL PRECURSOR (NSL-TP) (STEROL CARRIER PROTEIN 2) (SCP-2) (STEROL CARRIER PROTEIN X) (SCP-X) (SCPX). [SWISSPROT;Acc:P22307]" 0.192957 0.366703155 SCP2
0.526678 1234 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L2 (SNF2-ALPHA). [SWISSPROT;Acc:P51531] 0.130458 0.247699733 SMARCA2
1235 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L4 (SNF2-BETA) (BRG-1 PROTEIN) (MITOTIC GROWTH AND TRANSCRIPTION ACTIVATOR) (BRAHMA PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P51532] SMARCA4
0.526818 952 SIMILAR TO PUTATIVE TRANSMEMBRANE PROTEIN; HOMOLOG OF YEAST GOLGI MEMBRANE PROTEIN YIF1P (YIP1P-INTERACTING FACTOR). [RefSeq;Acc:NM_033557] 0.135079 0.256405438 YIF1B
0.527051 1287 GUANINE NUCLEOTIDE-BINDING PROTEIN-LIKE 1 (GTP-BINDING PROTEIN HSR1). [SWISSPROT;Acc:P36915] 0.129655 0.246000861 no value
0.527101 2513 PINCH PROTEIN (PARTICULARLY INTERESTING NEW CYS-HIS PROTEIN) (LIM AND SENESCENT CELL ANTIGEN-LIKE DOMAINS 1). [SWISSPROT;Acc:P48059] 0.113204 0.214767189 LIMS1
0.528466 2942 NUCLEOTIDE-BINDING PROTEIN 1 (NBP 1). [SWISSPROT;Acc:P53384] 0.0819552 0.155081311 NUBP1
2943 NUCLEOTIDE BINDING PROTEIN 2 (NBP 2). [SWISSPROT;Acc:Q9Y5Y2] NUBP2
0.528749 2263 NEUROTRYPSIN PRECURSOR (EC 3.4.21.-) (MOTOPSIN) (LEYDIN). [SWISSPROT;Acc:P56730] 0.11794 0.223054795 PRSS12
0.529029 2936 0.0831672 0.157207261 VPS37C

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/