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