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 Rank measured Gene description expected final
Results: HTML CSV LaTeX Showing element 601 to 650 of 3206 in total
Hugo
Rank
measured
description
expected
final
BAG1 1380 0.200609 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-1 (BCL-2 BINDING ATHANOGENE- 1) (BAG-1) (GLUCOCORTICOID RECEPTOR-ASSOCIATED PROTEIN RAP46). [SWISSPROT;Acc:Q99933] 0.819994 0.244646912
BAG2 1064 0.15369 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-2. [SWISSPROT;Acc:O95816] 0.608346 0.252635836
BAG3 1300 0.0975531 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-3 (BCL-2 BINDING ATHANOGENE- 3) (BAG-3) (BCL-2-BINDING PROTEIN BIS) (DOCKING PROTEIN CAIR-1). [SWISSPROT;Acc:O95817] 0.396904 0.245785127
BAIAP3 656 0.0241104 BAI1-ASSOCIATED PROTEIN 3; BAI-ASSOCIATED PROTEIN 3. [RefSeq;Acc:NM_003933] 0.0901025 0.26758858
BARD1 664 0.122728 BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1 (BARD-1). [SWISSPROT;Acc:Q99728] 0.45954 0.267067067
BARX1 869 0.139848 HOMEOBOX PROTEIN BARH-LIKE 1. [SWISSPROT;Acc:Q9HBU1] 0.537326 0.260266579
BARX2 875 0.109193 HOMEOBOX PROTEIN BARH-LIKE 2. [SWISSPROT;Acc:Q9UMQ3] 0.419545 0.260265287
BBOX1 1082 0.0513934 "GAMMA-BUTYROBETAINE,2-OXOGLUTARATE DIOXYGENASE (EC 1.14.11.1) (GAMMA-BUTYROBETAINE HYDROXYLASE) (GAMMA-BBH). [SWISSPROT;Acc:O75936]" 0.203883 0.252073003
BBS7 742 0.0385694 BARDET-BIEDL SYNDROME 7 PROTEIN ISOFORM A; BBS2-LIKE 1. [RefSeq;Acc:NM_176824] 0.145821 0.264498255
BCAR1 190 0.17117 CRK-ASSOCIATED SUBSTRATE (P130CAS) (BREAST CANCER ANTI-ESTROGEN RESISTANCE 1 PROTEIN). [SWISSPROT;Acc:P56945] 0.524421 0.326398066
BCAR3 188 0.157948 BREAST CANCER ANTIESTROGEN RESISTANCE 3. [RefSeq;Acc:NM_003567] 0.480256 0.328882929
BCAS2 519 0.0379775 "BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [RefSeq;Acc:NM_005872]" 0.139495 0.272249901
BCAT1 1461 0.471522 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, CYTOSOLIC (EC 2.6.1.42) (BCAT(C)) (ECA39 PROTEIN). [SWISSPROT;Acc:P54687]" 1.94005 0.243046313
BCAT2 1452 0.384181 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.42) (BCAT(M)) (PLACENTAL PROTEIN 18) (PP18). [SWISSPROT;Acc:O15382]" 1.57878 0.243340427
BCCIP 2015 0.0167203 BRCA2 AND CDKN1A-INTERACTING PROTEIN ISOFORM BCCIPALPHA; BRCA2 AND CDKN1A-INTERACTING PROTEIN; CDK INHIBITOR P21 BINDING PROTEIN; BCCIPALPHA; BCCIPBETA; TOK-1ALPHA; TOK-1BETA. [RefSeq;Acc:NM_016567] 0.0725001 0.230624509
BCKDHB 432 0.176985 "2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA CHAIN) (BCKDH E1-BETA). [SWISSPROT;Acc:P21953]" 0.63809 0.277366829
BCKDK 2537 1.13737 "[3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE, MITOCHONDRIAL PRECURSOR (EC 2.7.1.115) (BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE) (BCKDHKIN) (BCKD-KINASE). [SWISSPROT;Acc:O14874]" 5.29857 0.21465603
BCL3 1545 0.424367 B-CELL LYMPHOMA 3-ENCODED PROTEIN (BCL-3 PROTEIN). [SWISSPROT;Acc:P20749] 1.75491 0.241816959
BCL6 734 0.0869475 B-CELL LYMPHOMA 6 PROTEIN (BCL-6) (ZINC FINGER PROTEIN 51) (LAZ-3 PROTEIN) (BCL-5). [SWISSPROT;Acc:P41182] 0.328537 0.264650557
BCL6B 737 0.0692921 "B-CELL CLL/LYMPHOMA 6, MEMBER B (ZINC FINGER PROTEIN); ZINC FINGER PROTEIN 62. [RefSeq;Acc:NM_181844]" 0.261825 0.264650434
BCMO1 283 0.0549835 "BETA-CAROTENE 15, 15'-DIOXYGENASE; BETA-CAROTENE 15,15'-MONOOXYGENASE. [RefSeq;Acc:NM_017429]" 0.182179 0.301810307
BECN1 2063 0.0471781 BECLIN 1 (COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN) (PROTEIN GT197). [SWISSPROT;Acc:Q14457] 0.20547 0.229610649
BHLHB4 3053 0.0691801 BA305P22.3 (BREAST CARCINOMA AMPLIFIED SEQUENCE 4). [SPTREMBL;Acc:Q8NDY6] 0.65236 0.106045895
BHLHB5 3052 0.090943 "BASIC HELIX-LOOP-HELIX DOMAIN CONTAINING, CLASS B, 5; TRINUCLEOTIDE REPEAT CONTAINING 20. [RefSeq;Acc:NM_152414]" 0.857352 0.106074285
BIRC5 756 0.168097 BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5 (APOPTOSIS INHIBITOR SURVIVIN) (APOPTOSIS INHIBITOR 4). [SWISSPROT;Acc:O15392] 0.636394 0.264139825
BLOC1S1 1564 0.223546 GCN5-LIKE PROTEIN 1 (RT14 PROTEIN). [SWISSPROT;Acc:P78537] 0.927081 0.241128877
BOLA2B 2438 0.12244 MY016 PROTEIN. [SPTREMBL;Acc:Q9H3K6] 0.563645 0.21722893
BOP1 1265 0.872123 BLOCK OF PROLIFERATION 1. [SWISSPROT;Acc:Q14137] 3.53236 0.246895277
BPI 2159 0.0196608 BACTERICIDAL PERMEABILITY-INCREASING PROTEIN PRECURSOR (BPI) (CAP 57). [SWISSPROT;Acc:P17213] 0.0865184 0.227244147
BPIL2 2157 0.0141571 0.0622988 0.227245148
BRAF 2950 0.281099 B-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (P94) (V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1). [SWISSPROT;Acc:P15056] 1.90278 0.147730689
BRCA1 785 0.11358 BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN. [SWISSPROT;Acc:P38398] 0.432583 0.262562329
BRD2 537 0.105783 BROMODOMAIN-CONTAINING PROTEIN 2 (RING3 PROTEIN) (O27.1.1). [SWISSPROT;Acc:P25440] 0.390223 0.271083457
BRD3 536 0.122154 BROMODOMAIN-CONTAINING PROTEIN 3 (RING3-LIKE PROTEIN). [SWISSPROT;Acc:Q15059] 0.450566 0.271112334
BRD4 538 0.144761 BROMODOMAIN-CONTAINING PROTEIN 4 (HUNK1 PROTEIN). [SWISSPROT;Acc:O60885] 0.534019 0.27107837
BRD7 2460 0.26631 BROMODOMAIN CONTAINING 7; BROMODOMAIN PROTEIN; BROMODOMAIN-CONTAINING 7. [RefSeq;Acc:NM_013263] 1.22885 0.216714815
BRD9 2465 0.210228 0.970087 0.21671046
BRDT 544 0.0996239 TESTIS-SPECIFIC BROMODOMAIN PROTEIN. [RefSeq;Acc:NM_001726] 0.36752 0.27107069
BRF1 257 0.0376832 "TRANSCRIPTION FACTOR IIIB 90 KDA SUBUNIT (TFIIIB90) (HTFIIIB90) (B- RELATED FACTOR 1) (HBRF) (TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR, RNA POLYMERASE III, SUBUNIT 2) (TAF3B2). [SWISSPROT;Acc:Q92994]" 0.121057 0.311284767
BRP44 3010 0.0199967 BRAIN PROTEIN 44. [SWISSPROT;Acc:O95563] 0.163819 0.122065817
BRPF1 678 0.544593 TUBULIN TYROSINE LIGASE-LIKE PROTEIN HOTTL (HQP0207). [SWISSPROT;Acc:Q9Y4R7] 2.04792 0.265924938
BSCL2 2136 0.0629265 0.276021 0.227977219
BTAF1 1238 0.283008 TBP-ASSOCIATED FACTOR 172 (TAF-172) (TAF(II)170). [SWISSPROT;Acc:O14981] 1.14255 0.247698569
BTBD9 563 0.230346 0.850576 0.270811779
BTF3 239 0.737493 TRANSCRIPTION FACTOR BTF3 (RNA POLYMERASE B TRANSCRIPTION FACTOR 3). [SWISSPROT;Acc:P20290] 2.35516 0.313139235
BTF3L4 238 0.887185 2.82668 0.313861137
BUB1B 1132 0.116856 MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA (EC 2.7.1.-) (HBUBR1) (MAD3/BUB1-RELATED PROTEIN KINASE) (MITOTIC CHECKPOINT KINASE MAD3L). [SWISSPROT;Acc:O60566] 0.466478 0.250506991
BUB3 1636 0.153821 MITOTIC CHECKPOINT PROTEIN BUB3. [SWISSPROT;Acc:O43684] 0.64312 0.239179313
BUD13 1295 0.0401118 0.163123 0.245899107
BYSL 1591 0.784986 BYSTIN. [SWISSPROT;Acc:Q13895] 3.26689 0.240285409

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/